=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderdVlvGFI/inputs/gromacs_2026.3-1_arm64.buildinfo Source: gromacs Version: 2026.3-1 rebuilderd-worker node: codethink02-arm64 +------------------------------------------------------------------------------+ | Downloading sources Mon, 29 Jun 2026 16:20:31 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [57.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [151 kB] Get:7 https://deb.debian.org/debian sid InRelease [193 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6552 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:12 https://deb.debian.org/debian-security trixie-security/main Sources [182 kB] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [128 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [272 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [3376 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [7832 B] Get:18 https://deb.debian.org/debian forky/main Sources [11.0 MB] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.8 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.6 MB] Get:21 https://deb.debian.org/debian experimental/main Sources [393 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [2568 B] Fetched 34.9 MB in 3s (10.9 MB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.3-1.dsc' gromacs_2026.3-1.dsc 3252 SHA256:50e05686442252faf584a7b27eac5330cc06be11dd563c84489ab9061a266aae 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.3.orig-regressiontests.tar.gz' gromacs_2026.3.orig-regressiontests.tar.gz 16580747 SHA256:ec28a220729e8ad5e2a668919d201b3f283d37ecd3d6e7aa0f7c8a2fa278fa6a 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.3.orig.tar.gz' gromacs_2026.3.orig.tar.gz 45914529 SHA256:1094b7bbc6a3960223827114626657110b40096cdf9598a727935fc84ebf8aa0 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.3-1.debian.tar.xz' gromacs_2026.3-1.debian.tar.xz 13665824 SHA256:79054d93c2874a4cbcd727aad89d9dcfc8d4aec26a03e7b129a59d7a4d938861 ec28a220729e8ad5e2a668919d201b3f283d37ecd3d6e7aa0f7c8a2fa278fa6a gromacs_2026.3.orig-regressiontests.tar.gz 1094b7bbc6a3960223827114626657110b40096cdf9598a727935fc84ebf8aa0 gromacs_2026.3.orig.tar.gz 79054d93c2874a4cbcd727aad89d9dcfc8d4aec26a03e7b129a59d7a4d938861 gromacs_2026.3-1.debian.tar.xz 50e05686442252faf584a7b27eac5330cc06be11dd563c84489ab9061a266aae gromacs_2026.3-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Mon, 29 Jun 2026 16:20:36 +0000 | +------------------------------------------------------------------------------+ Rebuilding gromacs=2026.3-1 in /srv/rebuilderd/tmp/rebuilderdVlvGFI/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdVlvGFI/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdVlvGFI/inputs/gromacs_2026.3-1_arm64.buildinfo /srv/rebuilderd/tmp/rebuilderdVlvGFI/inputs/gromacs_2026.3-1_arm64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/gromacs-2026.3 I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [193 kB] Get:2 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable InRelease [193 kB] Get:3 http://deb.debian.org/debian unstable/main arm64 Packages [10.5 MB] Get:4 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 Packages [10.5 MB] Fetched 21.3 MB in 2s (10.3 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260628T204121Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-5+b1 [1440 B] Fetched 1440 B in 0s (140 kB/s) dpkg-name: info: moved 'gcc-aarch64-linux-gnu_4%3a15.2.0-5+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpd2a_ujk5/gcc-aarch64-linux-gnu_15.2.0-5+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 base-files arm64 14.2 [87.9 kB] Fetched 87.9 kB in 0s (7626 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8_6nh7sf/base-files_14.2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 perl-base arm64 5.40.1-8 [1525 kB] Fetched 1525 kB in 0s (77.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl_yeogx7/perl-base_5.40.1-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.14.0-2 [141 kB] Fetched 141 kB in 0s (12.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_puyowqx/libhwloc15_2.14.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libatomic1 arm64 16.1.0-2 [9780 B] Fetched 9780 B in 0s (919 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgkwq3bfx/libatomic1_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 binutils arm64 2.46.50.20260617-1 [279 kB] Fetched 279 kB in 0s (22.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy7ecycsw/binutils_2.46.50.20260617-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 63.0-1.1+b3 [681 kB] Fetched 681 kB in 0s (46.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzzubtyq_/libibverbs-dev_63.0-1.1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.22.0-1 [60.6 kB] Fetched 60.6 kB in 0s (4687 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5og52t3s/libpsl5t64_0.22.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-7+b2 [1812 kB] Fetched 1812 kB in 0s (76.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxxtejft5/liblapack3_3.12.1-7+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14-dev arm64 3.14.6-1 [5227 kB] Fetched 5227 kB in 0s (153 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2mmsg787/libpython3.14-dev_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.1-7+b2 [139 kB] Fetched 139 kB in 0s (3168 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppb_u37tm/libblas-dev_3.12.1-7+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bash arm64 5.3-3 [1503 kB] Fetched 1503 kB in 0s (74.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0it5y9bk/bash_5.3-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-sys1t64 arm64 4.1.3-6 [53.2 kB] Fetched 53.2 kB in 0s (4230 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5pzynqrn/libtss2-sys1t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.14.6-1 [25.7 kB] Fetched 25.7 kB in 0s (2454 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdgmqcgwf/python3-dev_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 2.5.1-4 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkxswzdk9/pkgconf_2.5.1-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gfortran-15 arm64 15.3.0-1 [22.2 kB] Fetched 22.2 kB in 0s (2158 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0npp3evw/gfortran-15_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblzma5 arm64 5.8.3-1 [324 kB] Fetched 324 kB in 0s (24.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzmmh562j/liblzma5_5.8.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.14.0-2 [239 kB] Fetched 239 kB in 0s (20.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbfdgsm79/libhwloc-dev_2.14.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpkgconf7 arm64 2.5.1-4 [45.5 kB] Fetched 45.5 kB in 0s (4233 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphaflzper/libpkgconf7_2.5.1-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtinfo6 arm64 6.6+20251231-1+b1 [343 kB] Fetched 343 kB in 0s (28.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpok85_6b3/libtinfo6_6.6+20251231-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.20 [3504 B] Fetched 3504 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvtjkclr4/mpi-default-dev_1.20_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.47-4 [345 kB] Fetched 345 kB in 0s (26.0 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.47-4_arm64.deb' to '/srv/rebuilderd/tmp/tmpqxlijgrx/libmagic-mgc_5.47-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Fetched 6020 B in 0s (383 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyqke4355/dh-strip-nondeterminism_1.15.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.13+dfsg-1 [173 kB] Fetched 173 kB in 0s (7095 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp56g6epu0/libldap2_2.6.13+dfsg-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libudev1 arm64 261.1-2 [128 kB] Fetched 128 kB in 0s (4034 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvdtidmif/libudev1_261.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.24.1-1 [1270 kB] Fetched 1270 kB in 0s (37.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8wldooy_/groff-base_1.24.1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-rc0t64 arm64 4.1.3-6 [31.0 kB] Fetched 31.0 kB in 0s (1153 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa2e6wru9/libtss2-rc0t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dash arm64 0.5.12-12+b1 [95.6 kB] Fetched 95.6 kB in 0s (4113 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxdh7h56r/dash_0.5.12-12+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 22 [12.2 kB] Fetched 12.2 kB in 0s (1202 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpazmba57k/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 autopoint all 1.0-1 [820 kB] Fetched 820 kB in 0s (28.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsoat_bvc/autopoint_1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.47-4 [43.2 kB] Fetched 43.2 kB in 0s (1942 kB/s) dpkg-name: info: moved 'file_1%3a5.47-4_arm64.deb' to '/srv/rebuilderd/tmp/tmpczy8aoxw/file_5.47-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 9.1.0-4 [45.7 kB] Fetched 45.7 kB in 0s (2225 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyki5i8ft/libjs-sphinxdoc_9.1.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 libclang-common-21-dev arm64 1:21.1.8-7+b3 [768 kB] Fetched 768 kB in 0s (48.5 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-7+b3_arm64.deb' to '/srv/rebuilderd/tmp/tmprbq612cq/libclang-common-21-dev_21.1.8-7+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-5+b1 [4636 B] Fetched 4636 B in 0s (197 kB/s) dpkg-name: info: moved 'cpp-aarch64-linux-gnu_4%3a15.2.0-5+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpythr8vv1/cpp-aarch64-linux-gnu_15.2.0-5+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgfortran-15-dev arm64 15.3.0-1 [410 kB] Fetched 410 kB in 0s (33.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn321ao4l/libgfortran-15-dev_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 make arm64 4.4.1-3+b1 [454 kB] Fetched 454 kB in 0s (18.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0v_mzplz/make_4.4.1-3+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 hostname arm64 3.25+b1 [11.2 kB] Fetched 11.2 kB in 0s (913 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqzrghlks/hostname_3.25+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 libllvm21 arm64 1:21.1.8-7+b3 [25.4 MB] Fetched 25.4 MB in 0s (114 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-7+b3_arm64.deb' to '/srv/rebuilderd/tmp/tmpl9v7q8gw/libllvm21_21.1.8-7+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 tpm-udev all 4.1.3-6 [27.4 kB] Fetched 27.4 kB in 0s (1434 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzjz558rt/tpm-udev_4.1.3-6_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-2.1+b1 [27.3 kB] Fetched 27.3 kB in 0s (1495 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyr_iywz7/libcbor0.10_0.10.2-2.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.14 arm64 3.14.6-1 [846 kB] Fetched 846 kB in 0s (58.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2hdrd0tu/python3.14_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 systemd arm64 261.1-2 [3121 kB] Fetched 3121 kB in 0s (64.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx8iwqt6g/systemd_261.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprj147m14/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-5+b1 [1204 B] Fetched 1204 B in 0s (120 kB/s) dpkg-name: info: moved 'g++-aarch64-linux-gnu_4%3a15.2.0-5+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmponw7xk7p/g++-aarch64-linux-gnu_15.2.0-5+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfftw3-bin arm64 3.3.11-1 [42.7 kB] Fetched 42.7 kB in 0s (1962 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpavevku00/libfftw3-bin_3.3.11-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.12.0-2+b1 [106 kB] Fetched 106 kB in 0s (5858 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1euuncwu/libnl-3-dev_3.12.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-esys-3.0.2-0t64 arm64 4.1.3-6 [139 kB] Fetched 139 kB in 0s (7924 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgsir_wxd/libtss2-esys-3.0.2-0t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.21.0-1 [810 kB] Fetched 810 kB in 0s (28.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7st5gm5v/libucx0_1.21.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbz2-1.0 arm64 1.0.8-6+b2 [36.6 kB] Fetched 36.6 kB in 0s (1947 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpde2vrav9/libbz2-1.0_1.0.8-6+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.69.0-1 [84.2 kB] Fetched 84.2 kB in 0s (4676 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph612c3nf/libnghttp2-14_1.69.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.195-1 [57.5 kB] Fetched 57.5 kB in 0s (4793 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiho3g_qz/libelf1t64_0.195-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.22.1-3 [125 kB] Fetched 125 kB in 0s (5559 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9vwxzxvi/libgssapi-krb5-2_1.22.1-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.12.0-2+b1 [181 kB] Fetched 181 kB in 0s (8487 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp9h306jc/libnl-route-3-200_3.12.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 mount arm64 2.42.2-1 [162 kB] Fetched 162 kB in 0s (6825 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgizq_7s8/mount_2.42.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.18-1 [18.3 kB] Fetched 18.3 kB in 0s (1520 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv5x6v3b5/libmunge2_0.5.18-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-4 [22.2 kB] Fetched 22.2 kB in 0s (857 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg_fqoy_y/libffi8_3.5.2-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libc-dev-bin arm64 2.42-17 [37.0 kB] Fetched 37.0 kB in 0s (1575 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1gdv15wh/libc-dev-bin_2.42-17_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-tcti-device0t64 arm64 4.1.3-6 [35.2 kB] Fetched 35.2 kB in 0s (1799 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpta6p5o12/libtss2-tcti-device0t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14-stdlib arm64 3.14.6-1 [2188 kB] Fetched 2188 kB in 0s (59.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplcbgk8eq/libpython3.14-stdlib_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 tar arm64 1.35+dfsg-4 [802 kB] Fetched 802 kB in 0s (35.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf9uxje1m/tar_1.35+dfsg-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmd0 arm64 1.2.0-2 [38.8 kB] Fetched 38.8 kB in 0s (1881 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfc6kzptg/libmd0_1.2.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libperl5.40 arm64 5.40.1-8 [4133 kB] Fetched 4133 kB in 0s (54.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpphu5ht6p/libperl5.40_5.40.1-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 zlib1g arm64 1:1.3.dfsg+really1.3.2-3 [87.9 kB] Fetched 87.9 kB in 0s (4626 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.2-3_arm64.deb' to '/srv/rebuilderd/tmp/tmpb5wgwz01/zlib1g_1.3.dfsg+really1.3.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b2 [126 kB] Fetched 126 kB in 0s (6184 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiqh4hplr/libevent-core-2.1-7t64_2.1.12-stable-10+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gcc-15-aarch64-linux-gnu arm64 15.3.0-1 [19.6 MB] Fetched 19.6 MB in 0s (111 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnfh7fd0l/gcc-15-aarch64-linux-gnu_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.11-1 [298 kB] Fetched 298 kB in 0s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpih7sn028/libfftw3-double3_3.3.11-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 6.4.3+dfsg-5 [385 kB] Fetched 385 kB in 0s (8795 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgjplrog8/libhsa-runtime64-1_6.4.3+dfsg-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpcre2-8-0 arm64 10.46-1+b2 [259 kB] Fetched 259 kB in 0s (11.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpck355q0u/libpcre2-8-0_10.46-1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libattr1 arm64 1:2.5.2-4 [22.7 kB] Fetched 22.7 kB in 0s (1016 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_arm64.deb' to '/srv/rebuilderd/tmp/tmpq9txf9za/libattr1_2.5.2-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libprrte-dev arm64 3.0.13-3 [3636 kB] Fetched 3636 kB in 0s (95.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfx_5h_nd/libprrte-dev_3.0.13-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam0g arm64 1.7.0-6 [64.7 kB] Fetched 64.7 kB in 0s (6231 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx6s7b1oi/libpam0g_1.7.0-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2+b2 [69.1 kB] Fetched 69.1 kB in 0s (3636 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv_yp8hj4/libuchardet0_0.0.8-2+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bzip2 arm64 1.0.8-6+b2 [39.2 kB] Fetched 39.2 kB in 0s (1697 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwprucjra/bzip2_1.0.8-6+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 libdrm-amdgpu1 arm64 2.4.134-2 [22.1 kB] Fetched 22.1 kB in 0s (1037 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxsr4z5xm/libdrm-amdgpu1_2.4.134-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.3.0-1 [10.8 MB] Fetched 10.8 MB in 0s (81.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj6_cpcq4/gfortran-15-aarch64-linux-gnu_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 261.1-2 [2265 kB] Fetched 2265 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt_irn0hw/libsystemd-shared_261.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.22.1-1 [120 kB] Fetched 120 kB in 0s (5337 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpft211tir/libngtcp2-16_1.22.1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-4 [99.2 kB] Fetched 99.2 kB in 0s (9667 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaf0j54j7/dwz_0.16-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.22.1-3 [30.2 kB] Fetched 30.2 kB in 0s (1330 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqflqijvr/libkrb5support0_1.22.1-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 binutils-aarch64-linux-gnu arm64 2.46.50.20260617-1 [879 kB] Fetched 879 kB in 0s (50.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjuvz36w6/binutils-aarch64-linux-gnu_2.46.50.20260617-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.14.6-1 [8108 B] Fetched 8108 B in 0s (345 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_pyzfvbn/libpython3-stdlib_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.13-1 [799 kB] Fetched 799 kB in 0s (56.1 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpdtkpi59p/libx11-6_1.8.13-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libitm1 arm64 16.1.0-2 [24.3 kB] Fetched 24.3 kB in 0s (2368 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi6ic6t46/libitm1_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 5.0.10-1 [30.3 kB] Fetched 30.3 kB in 0s (1408 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuqrs9657/openmpi-common_5.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 perl-modules-5.40 all 5.40.1-8 [3019 kB] Fetched 3019 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpihvs3_n4/perl-modules-5.40_5.40.1-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 python3-numpy arm64 1:2.4.6+ds-1 [4337 kB] Fetched 4337 kB in 0s (129 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.4.6+ds-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpxtvltmdd/python3-numpy_2.4.6+ds-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gzip arm64 1.13-1+b1 [135 kB] Fetched 135 kB in 0s (5586 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdpyob7fj/gzip_1.13-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 python3-numpy-dev arm64 1:2.4.6+ds-1 [132 kB] Fetched 132 kB in 0s (11.5 MB/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.4.6+ds-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpmsa4phys/python3-numpy-dev_2.4.6+ds-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjansson4 arm64 2.15.0-1 [61.5 kB] Fetched 61.5 kB in 0s (2994 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcueaziip/libjansson4_2.15.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblsan0 arm64 16.1.0-2 [1212 kB] Fetched 1212 kB in 0s (49.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoeyrtxcg/liblsan0_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-4 [168 kB] Fetched 168 kB in 0s (7376 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfyytiqa2/libreadline8t64_8.3-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.4.2-5 [23.9 MB] Fetched 23.9 MB in 0s (154 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxqnvczhw/python3-networkx_3.4.2-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libcrypt1 arm64 1:4.5.1-1+b1 [92.4 kB] Fetched 92.4 kB in 0s (4870 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpz6llsxnd/libcrypt1_4.5.1-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 binutils-common arm64 2.46.50.20260617-1 [2636 kB] Fetched 2636 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz4pr8aep/binutils-common_2.46.50.20260617-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libprrte3 arm64 3.0.13-3 [389 kB] Fetched 389 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplbajdd61/libprrte3_3.0.13-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 3.0.1-3 [240 kB] Fetched 240 kB in 0s (8257 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp_nodiwe/pybind11-dev_3.0.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 diffutils arm64 1:3.12-1+b1 [398 kB] Fetched 398 kB in 0s (3888 kB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpuargrlua/diffutils_3.12-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 g++-15 arm64 15.3.0-1 [28.7 kB] Fetched 28.7 kB in 0s (1505 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqugu5s5j/g++-15_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.8.7-1 [327 kB] Fetched 327 kB in 0s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_8m8b5sj/libarchive13t64_3.8.7-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.4.2-1 [455 kB] Fetched 455 kB in 0s (21.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi5s6ly8h/libunistring5_1.4.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfuse3-4 arm64 3.18.2-2 [95.6 kB] Fetched 95.6 kB in 0s (4725 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxnys1tny/libfuse3-4_3.18.2-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20260512-1 [88.3 kB] Fetched 88.3 kB in 0s (8318 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4dkrhksl/libedit2_3.1-20260512-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 findutils arm64 4.10.0-4 [694 kB] Fetched 694 kB in 0s (50.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp56b8vhhy/findutils_4.10.0-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libuuid1 arm64 2.42.2-1 [32.8 kB] Fetched 32.8 kB in 0s (1703 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplqqbcgzt/libuuid1_2.42.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 63.0-1.1+b3 [59.9 kB] Fetched 59.9 kB in 0s (2318 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplakpyxof/libibverbs1_63.0-1.1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 base-passwd arm64 3.6.8+b1 [54.3 kB] Fetched 54.3 kB in 0s (4361 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvvqp_9bp/base-passwd_3.6.8+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.6+b2 [2632 B] Fetched 2632 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwquzwwpl/architecture-properties_0.2.6+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (1663 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplp2llcnh/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfftw3-single3 arm64 3.3.11-1 [459 kB] Fetched 459 kB in 0s (33.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp42n3enb3/libfftw3-single3_3.3.11-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmpfr6 arm64 4.2.2-3 [691 kB] Fetched 691 kB in 0s (44.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppdt0tgv2/libmpfr6_4.2.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-9+b2 [60.1 kB] Fetched 60.1 kB in 0s (2375 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-9+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpddv7_133/libproc2-0_4.0.4-9+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 libcurl4t64 arm64 8.21.0-1 [380 kB] Fetched 380 kB in 0s (28.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ffpq1ax/libcurl4t64_8.21.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1+b3 [14.0 kB] Fetched 14.0 kB in 0s (1312 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1l9hqr4p/libxnvctrl0_535.171.04-1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Fetched 12.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp17prae4x/netbase_6.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 3.0.1-3 [251 kB] Fetched 251 kB in 0s (21.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptjdix0cc/python3-pybind11_3.0.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgcc-s1 arm64 16.1.0-2 [53.2 kB] Fetched 53.2 kB in 0s (4610 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3hxvrsb_/libgcc-s1_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (660 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmpsx3aof7k/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libucc1 arm64 1.8.0-2 [333 kB] Fetched 333 kB in 0s (26.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdcppz1ji/libucc1_1.8.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libamd-comgr3 arm64 7.0.2+dfsg-3 [12.8 MB] Fetched 12.8 MB in 0s (180 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgmn7kmd5/libamd-comgr3_7.0.2+dfsg-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 2.1.0-2 [7540 B] Fetched 7540 B in 0s (686 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcokt_g70/python3-iniconfig_2.1.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 libdrm2 arm64 2.4.134-2 [37.1 kB] Fetched 37.1 kB in 0s (3358 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0rax6f5p/libdrm2_2.4.134-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libselinux1 arm64 3.10-1 [79.9 kB] Fetched 79.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjfae58pe/libselinux1_3.10-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmuparser2v5 arm64 2.3.4-2+b1 [127 kB] Fetched 127 kB in 0s (6428 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ipdu8_t/libmuparser2v5_2.3.4-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.17.0-1 [74.5 kB] Fetched 74.5 kB in 0s (7419 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiap0t504/libfido2-1_1.17.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sed arm64 4.9-3 [326 kB] Fetched 326 kB in 0s (16.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp066m8iu3/sed_4.9-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhwasan0 arm64 16.1.0-2 [1505 kB] Fetched 1505 kB in 0s (51.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj5w52bvm/libhwasan0_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libctf-nobfd0 arm64 2.46.50.20260617-1 [155 kB] Fetched 155 kB in 0s (7917 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7uf5i0gz/libctf-nobfd0_2.46.50.20260617-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam-modules arm64 1.7.0-6 [161 kB] Fetched 161 kB in 0s (5858 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2hpy8qql/libpam-modules_1.7.0-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.1-7+b2 [3744 kB] Fetched 3744 kB in 0s (73.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5dgzt88f/liblapack-dev_3.12.1-7+b2_arm64.deb' Downloading dependency 1 of 301: gcc-aarch64-linux-gnu:arm64=4:15.2.0-5+b1 Downloading dependency 2 of 301: base-files:arm64=14.2 Downloading dependency 3 of 301: perl-base:arm64=5.40.1-8 Downloading dependency 4 of 301: libhwloc15:arm64=2.14.0-2 Downloading dependency 5 of 301: libatomic1:arm64=16.1.0-2 Downloading dependency 6 of 301: binutils:arm64=2.46.50.20260617-1 Downloading dependency 7 of 301: libibverbs-dev:arm64=63.0-1.1+b3 Downloading dependency 8 of 301: libpsl5t64:arm64=0.22.0-1 Downloading dependency 9 of 301: liblapack3:arm64=3.12.1-7+b2 Downloading dependency 10 of 301: libpython3.14-dev:arm64=3.14.6-1 Downloading dependency 11 of 301: libblas-dev:arm64=3.12.1-7+b2 Downloading dependency 12 of 301: bash:arm64=5.3-3 Downloading dependency 13 of 301: libtss2-sys1t64:arm64=4.1.3-6 Downloading dependency 14 of 301: python3-dev:arm64=3.14.6-1 Downloading dependency 15 of 301: pkgconf:arm64=2.5.1-4 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Downloading dependency 94 of 301: binutils-common:arm64=2.46.50.20260617-1 Downloading dependency 95 of 301: libprrte3:arm64=3.0.13-3 Downloading dependency 96 of 301: pybind11-dev:arm64=3.0.1-3 Downloading dependency 97 of 301: diffutils:arm64=1:3.12-1+b1 Downloading dependency 98 of 301: g++-15:arm64=15.3.0-1 Downloading dependency 99 of 301: libarchive13t64:arm64=3.8.7-1 Downloading dependency 100 of 301: libunistring5:arm64=1.4.2-1 Downloading dependency 101 of 301: libfuse3-4:arm64=3.18.2-2 Downloading dependency 102 of 301: libedit2:arm64=3.1-20260512-1 Downloading dependency 103 of 301: findutils:arm64=4.10.0-4 Downloading dependency 104 of 301: libuuid1:arm64=2.42.2-1 Downloading dependency 105 of 301: libibverbs1:arm64=63.0-1.1+b3 Downloading dependency 106 of 301: base-passwd:arm64=3.6.8+b1 Downloading dependency 107 of 301: architecture-properties:arm64=0.2.6+b2 Downloading dependency 108 of 301: init-system-helpers:arm64=1.69 Downloading dependency 109 of 301: libfftw3-single3:arm64=3.3.11-1 Downloading dependency 110 of 301: libmpfr6:arm64=4.2.2-3 Downloading dependency 111 of 301: libproc2-0:arm64=2:4.0.4-9+b2 Downloading dependency 112 of 301: libcurl4t64:arm64=8.21.0-1 Downloading dependency 113 of 301: libxnvctrl0:arm64=535.171.04-1+b3 Downloading dependency 114 of 301: netbase:arm64=6.5 Downloading dependency 115 of 301: python3-pybind11:arm64=3.0.1-3 Downloading dependency 116 of 301: libgcc-s1:arm64=16.1.0-2 Downloading dependency 117 of 301: libaudit-common:arm64=1:4.1.2-1 Downloading dependency 118 of 301: libucc1:arm64=1.8.0-2 Downloading dependency 119 of 301: libamd-comgr3:arm64=7.0.2+dfsg-3 Downloading dependency 120 of 301: python3-iniconfig:arm64=2.1.0-2 Downloading dependency 121 of 301: libdrm2:arm64=2.4.134-2 Downloading dependency 122 of 301: libselinux1:arm64=3.10-1 Downloading dependency 123 of 301: libmuparser2v5:arm64=2.3.4-2+b1 Downloading dependency 124 of 301: libfido2-1:arm64=1.17.0-1 Downloading dependency 125 of 301: sed:arm64=4.9-3 Downloading dependency 126 of 301: libhwasan0:arm64=16.1.0-2 Downloading dependency 127 of 301: libctf-nobfd0:arm64=2.46.50.20260617-1 Downloading dependency 128 of 301: libpam-modules:arm64=1.7.0-6 Downloading dependency 129 of 301: liblapack-dev:arm64=3.12.1-7+b2 Downloading dependency 130 of 301: libevent-dev:arm64=2.1.12-stable-10+b2Get:1 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-10+b2 [303 kB] Fetched 303 kB in 0s (24.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptqid5u64/libevent-dev_2.1.12-stable-10+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.12.0-2+b1 [58.8 kB] Fetched 58.8 kB in 0s (4012 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppkur7nre/libnl-3-200_3.12.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libc6-dev arm64 2.42-17 [1615 kB] Fetched 1615 kB in 0s (85.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdnpzn92m/libc6-dev_2.42-17_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 g++ arm64 4:15.2.0-5+b1 [1336 B] Fetched 1336 B in 0s (65.8 kB/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmph_dark06/g++_15.2.0-5+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 63.0-1.1+b3 [356 kB] Fetched 356 kB in 0s (16.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp3hy63e3/ibverbs-providers_63.0-1.1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.8.2-1 [108 kB] Fetched 108 kB in 0s (10.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxjtuj45c/libexpat1_2.8.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.8.2-1 [161 kB] Fetched 161 kB in 0s (15.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp2qyj7bc/libexpat1-dev_2.8.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 16.1.0-2 [367 kB] Fetched 367 kB in 0s (12.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxd_ejhwn/libgfortran5_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1+b1 [1455 kB] Fetched 1455 kB in 0s (84.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl4gp4s5g/man-db_2.13.1-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 grep arm64 3.12-1+b1 [440 kB] Fetched 440 kB in 0s (16.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgdqg_wgp/grep_3.12-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtsan2 arm64 16.1.0-2 [2448 kB] Fetched 2448 kB in 0s (68.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6n2fvzb_/libtsan2_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsmartcols1 arm64 2.42.2-1 [138 kB] Fetched 138 kB in 0s (6602 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzl5yxp2v/libsmartcols1_2.42.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.5.4-11 [415 kB] Fetched 415 kB in 0s (20.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpas8yam_b/libltdl7_2.5.4-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 openssl-provider-legacy arm64 3.6.3-1 [317 kB] Fetched 317 kB in 0s (14.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg6r8m6ur/openssl-provider-legacy_3.6.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 2.5.1-4 [35.1 kB] Fetched 35.1 kB in 0s (1983 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu8ogpfjf/pkgconf-bin_2.5.1-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libssl3t64 arm64 3.6.3-1 [2775 kB] Fetched 2775 kB in 0s (79.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuy7ro6oi/libssl3t64_3.6.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 tzdata all 2026b-1 [260 kB] Fetched 260 kB in 0s (23.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt8lobkke/tzdata_2026b-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Fetched 319 kB in 0s (27.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjr6_orpj/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgprofng0 arm64 2.46.50.20260617-1 [679 kB] Fetched 679 kB in 0s (45.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6azh2onc/libgprofng0_2.46.50.20260617-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 build-essential arm64 12.12 [4624 B] Fetched 4624 B in 0s (243 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu71qsohk/build-essential_12.12_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libstdc++6 arm64 16.1.0-2 [701 kB] Fetched 701 kB in 0s (27.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu1g03p0i/libstdc++6_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dpkg arm64 1.23.7 [1512 kB] Fetched 1512 kB in 0s (75.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_f_wnpu/dpkg_1.23.7_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.15.0-1 [61.9 kB] Fetched 61.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo32jzw5x/libnghttp3-9_1.15.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.6.0-2 [27.2 kB] Fetched 27.2 kB in 0s (1395 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5sj333_/python3-pluggy_1.6.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.19-1+b2 [21.5 kB] Fetched 21.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph6hi8fnk/libnuma1_2.0.19-1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsframe3 arm64 2.46.50.20260617-1 [85.0 kB] Fetched 85.0 kB in 0s (3655 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5_zz4akx/libsframe3_2.46.50.20260617-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.14-dev arm64 3.14.6-1 [508 kB] Fetched 508 kB in 0s (18.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzekpov1h/python3.14-dev_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libacl1 arm64 2.3.2-3 [31.8 kB] Fetched 31.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgxwef6za/libacl1_2.3.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 patch arm64 2.8-2+b1 [128 kB] Fetched 128 kB in 0s (8292 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqcm4173i/patch_2.8-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14-minimal arm64 3.14.6-1 [889 kB] Fetched 889 kB in 0s (32.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzp2lc30y/libpython3.14-minimal_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libcc1-0 arm64 16.1.0-2 [43.6 kB] Fetched 43.6 kB in 0s (2328 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpntj0ar_h/libcc1-0_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1.1 [7361 kB] Fetched 7361 kB in 0s (98.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplcx5o5uz/libz3-4_4.13.3-1.1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.47-4 [104 kB] Fetched 104 kB in 0s (4794 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.47-4_arm64.deb' to '/srv/rebuilderd/tmp/tmpjxdxw89l/libmagic1t64_5.47-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gcc arm64 4:15.2.0-5+b1 [5156 B] Fetched 5156 B in 0s (251 kB/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp53utkpf7/gcc_15.2.0-5+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-7+b2 [129 kB] Fetched 129 kB in 0s (6812 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxesd0e0p/libblas3_3.12.1-7+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnettle8t64 arm64 3.10.2-1+b1 [304 kB] Fetched 304 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpygs9_scl/libnettle8t64_3.10.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.6-1.1+b1 [128 kB] Fetched 128 kB in 0s (5699 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvgz7kx9z/librhash1_1.4.6-1.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libibmad5 arm64 63.0-1.1+b3 [41.2 kB] Fetched 41.2 kB in 0s (2275 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp11u5te3_/libibmad5_63.0-1.1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblz4-1 arm64 1.10.0-10 [66.5 kB] Fetched 66.5 kB in 0s (6222 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxxlprnnb/liblz4-1_1.10.0-10_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.73-2 [516 kB] Fetched 516 kB in 0s (38.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyjj58zo5/autoconf_2.73-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgomp1 arm64 16.1.0-2 [132 kB] Fetched 132 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5gv2sr8b/libgomp1_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.7-4 [76.3 kB] Fetched 76.3 kB in 0s (3500 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9w51voqh/libjsoncpp26_1.9.7-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-11 [52.4 kB] Fetched 52.4 kB in 0s (2177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyjdbykq9/libsasl2-2_2.1.28+dfsg1-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.14.6-1 [8344 B] Fetched 8344 B in 0s (710 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7thsjnah/libpython3-dev_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Fetched 17.1 kB in 0s (950 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1vf54ibn/libfile-stripnondeterminism-perl_1.15.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-11+b1 [626 kB] Fetched 626 kB in 0s (50.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvwztd6r7/libdb5.3t64_5.3.28+dfsg2-11+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libamdhip64-6 arm64 6.4.3-5 [9338 kB] Fetched 9338 kB in 0s (175 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2lcg55ae/libamdhip64-6_6.4.3-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libopenmpi40 arm64 5.0.10-1 [1755 kB] Fetched 1755 kB in 0s (43.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9w11r6e5/libopenmpi40_5.0.10-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libboost1.90-dev arm64 1.90.0-6 [11.3 MB] Fetched 11.3 MB in 0s (119 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppm1qqz8b/libboost1.90-dev_1.90.0-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-3 [47.2 kB] Fetched 47.2 kB in 0s (2532 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg2g1y0wc/libpipeline1_1.5.8-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 systemd-tpm arm64 261.1-2 [148 kB] Fetched 148 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphiphhdx8/systemd-tpm_261.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbinutils arm64 2.46.50.20260617-1 [685 kB] Fetched 685 kB in 0s (28.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplu6ejg50/libbinutils_2.46.50.20260617-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 debianutils arm64 5.23.2+b1 [92.6 kB] Fetched 92.6 kB in 0s (4784 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw8bxv6dk/debianutils_5.23.2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6+b2 [9444 B] Fetched 9444 B in 0s (420 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2zj_blph/libkeyutils1_1.6.3-6+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfftw3-long3 arm64 3.3.11-1 [475 kB] Fetched 475 kB in 0s (40.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfa231gbn/libfftw3-long3_3.3.11-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 63.0-1.1+b3 [68.7 kB] Fetched 68.7 kB in 0s (6780 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcxo50fsk/librdmacm1t64_63.0-1.1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxxhash0 arm64 0.8.3-2+b2 [21.5 kB] Fetched 21.5 kB in 0s (1115 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2hz6n_ep/libxxhash0_0.8.3-2+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.21-1 [323 kB] Fetched 323 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0_mpbsgt/m4_1.4.21-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgcc-15-dev arm64 15.3.0-1 [2372 kB] Fetched 2372 kB in 0s (69.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi3rzf5h6/libgcc-15-dev_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b4 [49.0 kB] Fetched 49.0 kB in 0s (2645 kB/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b4_arm64.deb' to '/srv/rebuilderd/tmp/tmplwcgaez6/libxext6_1.3.4-1+b4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmpc3 arm64 1.3.1-3 [49.3 kB] Fetched 49.3 kB in 0s (4739 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdldg0s0d/libmpc3_1.3.1-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgdbm-compat4t64 arm64 1.26-1+b2 [52.0 kB] Fetched 52.0 kB in 0s (5003 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3pll0dhg/libgdbm-compat4t64_1.26-1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-mu-4.0.1-0t64 arm64 4.1.3-6 [67.0 kB] Fetched 67.0 kB in 0s (2994 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1e62rik3/libtss2-mu-4.0.1-0t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 5.0.10-1 [152 kB] Fetched 152 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc38aefwl/openmpi-bin_5.0.10-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:10.3p1-5 [919 kB] Fetched 919 kB in 0s (33.0 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.3p1-5_arm64.deb' to '/srv/rebuilderd/tmp/tmp4c5i8zx8/openssh-client_10.3p1-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gcc-15 arm64 15.3.0-1 [535 kB] Fetched 535 kB in 0s (38.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp48jsgy75/gcc-15_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 2.1.0-1.1+b2 [542 kB] Fetched 542 kB in 0s (21.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2c82t4mi/libfabric1_2.1.0-1.1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.19.2+dfsg-1 [847 kB] Fetched 847 kB in 0s (30.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc5y31u0n/python3-pygments_2.19.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1+b2 [20.8 kB] Fetched 20.8 kB in 0s (1117 kB/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpqr67oofz/libxau6_1.0.11-1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libc6 arm64 2.42-17 [1384 kB] Fetched 1384 kB in 0s (41.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg7abu7ty/libc6_2.42-17_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libc-bin arm64 2.42-17 [531 kB] Fetched 531 kB in 0s (33.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpounh1819/libc-bin_2.42-17_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Fetched 60.0 kB in 0s (3218 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpep0736u4/autotools-dev_20240727.1+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-tcti-swtpm0t64 arm64 4.1.3-6 [35.3 kB] Fetched 35.3 kB in 0s (1894 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwlsw0zgr/libtss2-tcti-swtpm0t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.12.0-2+b1 [214 kB] Fetched 214 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa_w10bfj/libnl-route-3-dev_3.12.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 perl arm64 5.40.1-8 [264 kB] Fetched 264 kB in 0s (10.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcjym6cda/perl_5.40.1-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 linux-libc-dev all 7.0.13-1 [2021 kB] Fetched 2021 kB in 0s (61.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpil2nfq1c/linux-libc-dev_7.0.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam-modules-bin arm64 1.7.0-6 [44.4 kB] Fetched 44.4 kB in 0s (2387 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi4cjb93g/libpam-modules-bin_1.7.0-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libblkid1 arm64 2.42.2-1 [165 kB] Fetched 165 kB in 0s (7458 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8tnpopfl/libblkid1_2.42.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.3+dfsg-1 [593 kB] Fetched 593 kB in 0s (27.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmaz99dnw/libxml2-16_2.15.3+dfsg-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libc-gconv-modules-extra arm64 2.42-17 [1129 kB] Fetched 1129 kB in 0s (39.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxojq4vo9/libc-gconv-modules-extra_2.42-17_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsqlite3-0 arm64 3.53.3-1 [900 kB] Fetched 900 kB in 0s (54.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5mh8q3hf/libsqlite3-0_3.53.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 0s (1288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwwui7_m0/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-11 [17.1 kB] Fetched 17.1 kB in 0s (816 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaqn615n4/libsasl2-modules-db_2.1.28+dfsg1-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgmp10 arm64 2:6.3.0+dfsg-5+b2 [543 kB] Fetched 543 kB in 0s (35.9 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmp30ye7e_9/libgmp10_6.3.0+dfsg-5+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmuparser-dev arm64 2.3.4-2+b1 [33.5 kB] Fetched 33.5 kB in 0s (1729 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe19p0ujw/libmuparser-dev_2.3.4-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.13-1 [346 kB] Fetched 346 kB in 0s (25.0 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmpeg58rhx7/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 mpi-default-bin arm64 1.20 [2724 B] Fetched 2724 B in 0s (126 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7zdf5jxv/mpi-default-bin_1.20_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 ncurses-bin arm64 6.6+20251231-1+b1 [435 kB] Fetched 435 kB in 0s (30.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_k9bkob/ncurses-bin_6.6+20251231-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.2-3 [916 kB] Fetched 916 kB in 0s (62.5 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_arm64.deb' to '/srv/rebuilderd/tmp/tmpg_1j6orw/zlib1g-dev_1.3.dfsg+really1.3.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libisl23 arm64 0.27-2 [598 kB] Fetched 598 kB in 0s (23.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj1lo7hln/libisl23_0.27-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfftw3-dev arm64 3.3.11-1 [1123 kB] Fetched 1123 kB in 0s (37.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgf10kvax/libfftw3-dev_3.3.11-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bash-completion all 1:2.16.0-8 [319 kB] Fetched 319 kB in 0s (29.4 MB/s) dpkg-name: info: moved 'bash-completion_1%3a2.16.0-8_all.deb' to '/srv/rebuilderd/tmp/tmpo68moyaq/bash-completion_2.16.0-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.19-1+b2 [37.1 kB] Fetched 37.1 kB in 0s (1987 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphqml26ni/libnuma-dev_2.0.19-1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.14.0-2 [16.2 kB] Fetched 16.2 kB in 0s (656 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy57aprc4/libhwloc-plugins_2.14.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dpkg-dev all 1.23.7 [1318 kB] Fetched 1318 kB in 0s (47.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpng1vjf1l/dpkg-dev_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (10.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9lnrer4_/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 g++-15-aarch64-linux-gnu arm64 15.3.0-1 [11.1 MB] Fetched 11.1 MB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpourb0msr/g++-15-aarch64-linux-gnu_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cpp arm64 4:15.2.0-5+b1 [1576 B] Fetched 1576 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpndxg5o7n/cpp_15.2.0-5+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b2 [170 kB] Fetched 170 kB in 0s (14.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5lbmi6k2/libevent-2.1-7t64_2.1.12-stable-10+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdpkg-perl all 1.23.7 [669 kB] Fetched 669 kB in 0s (46.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp07n4e2io/libdpkg-perl_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-4 [877 kB] Fetched 877 kB in 0s (34.2 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmp40ig97kd/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cpp-15 arm64 15.3.0-1 [1280 B] Fetched 1280 B in 0s (51.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpguuvps1e/cpp-15_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-5 [107 kB] Fetched 107 kB in 0s (5483 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9pbk34tf/libidn2-0_2.3.8-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b4 [50.8 kB] Fetched 50.8 kB in 0s (2723 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_f7uwfeg/libpciaccess0_0.17-3+b4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cpp-15-aarch64-linux-gnu arm64 15.3.0-1 [10.2 MB] Fetched 10.2 MB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps7cmp6ex/cpp-15-aarch64-linux-gnu_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libctf0 arm64 2.46.50.20260617-1 [86.1 kB] Fetched 86.1 kB in 0s (3722 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpegsoz54w/libctf0_2.46.50.20260617-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 libcap-ng0 arm64 0.9.3-1 [17.8 kB] Fetched 17.8 kB in 0s (938 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpndlidko5/libcap-ng0_0.9.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gettext arm64 1.0-1 [2547 kB] Fetched 2547 kB in 0s (53.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz8dfcboe/gettext_1.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b2 [102 kB] Fetched 102 kB in 0s (5256 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqw2sm_xn/libevent-extra-2.1-7t64_2.1.12-stable-10+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 1.0-1 [329 kB] Fetched 329 kB in 0s (14.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2_quv13s/gettext-base_1.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.4-1 [19.2 kB] Fetched 19.2 kB in 0s (1168 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfkl6cmfl/libcom-err2_1.47.4-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b2 [54.4 kB] Fetched 54.4 kB in 0s (2914 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0852jvqf/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libgdbm6t64 arm64 1.26-1+b2 [76.1 kB] Fetched 76.1 kB in 0s (4081 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0lrjv10e/libgdbm6t64_1.26-1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 cmake arm64 4.3.4-1 [13.7 MB] Fetched 13.7 MB in 0s (111 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpany3xewi/cmake_4.3.4-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libncursesw6 arm64 6.6+20251231-1+b1 [125 kB] Fetched 125 kB in 0s (12.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpirp1fa14/libncursesw6_6.6+20251231-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (1217 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbircpatg/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libprrte-bin arm64 3.0.13-3 [49.2 kB] Fetched 49.2 kB in 0s (2299 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppadarj1j/libprrte-bin_3.0.13-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b2 [60.5 kB] Fetched 60.5 kB in 0s (5338 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj7h4ddv_/libevent-openssl-2.1-7t64_2.1.12-stable-10+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpython3.14 arm64 3.14.6-1 [2240 kB] Fetched 2240 kB in 0s (52.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcmdetjfv/libpython3.14_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gcc-15-base arm64 15.3.0-1 [37.4 kB] Fetched 37.4 kB in 0s (2004 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8xj0mnaf/gcc-15-base_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 dh-python all 7.20260623 [114 kB] Fetched 114 kB in 0s (9019 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz03rhexs/dh-python_7.20260623_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.90.0.2 [3064 B] Fetched 3064 B in 0s (213 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmgw2abno/libboost-dev_1.90.0.2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-mpi4py arm64 4.1.2-1 [930 kB] Fetched 930 kB in 0s (58.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4d66in3m/python3-mpi4py_4.1.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (20.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphhjozsac/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libasan8 arm64 16.1.0-2 [2672 kB] Fetched 2672 kB in 0s (111 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_0gg9a9/libasan8_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 gcc-16-base arm64 16.1.0-2 [36.8 kB] Fetched 36.8 kB in 0s (1969 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbm_22689/gcc-16-base_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 coreutils arm64 9.10-1 [3049 kB] Fetched 3049 kB in 0s (69.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqrsdny1r/coreutils_9.10-1_arm64.deb' Downloading dependency 131 of 301: libnl-3-200:arm64=3.12.0-2+b1 Downloading dependency 132 of 301: libc6-dev:arm64=2.42-17 Downloading dependency 133 of 301: g++:arm64=4:15.2.0-5+b1 Downloading dependency 134 of 301: ibverbs-providers:arm64=63.0-1.1+b3 Downloading dependency 135 of 301: libexpat1:arm64=2.8.2-1 Downloading dependency 136 of 301: libexpat1-dev:arm64=2.8.2-1 Downloading dependency 137 of 301: libgfortran5:arm64=16.1.0-2 Downloading dependency 138 of 301: man-db:arm64=2.13.1-1+b1 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301: mpi-default-bin:arm64=1.20 Downloading dependency 217 of 301: ncurses-bin:arm64=6.6+20251231-1+b1 Downloading dependency 218 of 301: zlib1g-dev:arm64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 219 of 301: libisl23:arm64=0.27-2 Downloading dependency 220 of 301: libfftw3-dev:arm64=3.3.11-1 Downloading dependency 221 of 301: bash-completion:arm64=1:2.16.0-8 Downloading dependency 222 of 301: libnuma-dev:arm64=2.0.19-1+b2 Downloading dependency 223 of 301: libhwloc-plugins:arm64=2.14.0-2 Downloading dependency 224 of 301: dpkg-dev:arm64=1.23.7 Downloading dependency 225 of 301: libarchive-zip-perl:arm64=1.68-1 Downloading dependency 226 of 301: g++-15-aarch64-linux-gnu:arm64=15.3.0-1 Downloading dependency 227 of 301: cpp:arm64=4:15.2.0-5+b1 Downloading dependency 228 of 301: libevent-2.1-7t64:arm64=2.1.12-stable-10+b2 Downloading dependency 229 of 301: libdpkg-perl:arm64=1.23.7 Downloading dependency 230 of 301: automake:arm64=1:1.18.1-4 Downloading dependency 231 of 301: cpp-15:arm64=15.3.0-1 Downloading dependency 232 of 301: libidn2-0:arm64=2.3.8-5 Downloading dependency 233 of 301: libpciaccess0:arm64=0.17-3+b4 Downloading dependency 234 of 301: cpp-15-aarch64-linux-gnu:arm64=15.3.0-1 Downloading dependency 235 of 301: libctf0:arm64=2.46.50.20260617-1 Downloading dependency 236 of 301: libcap-ng0:arm64=0.9.3-1 Downloading dependency 237 of 301: gettext:arm64=1.0-1 Downloading dependency 238 of 301: libevent-extra-2.1-7t64:arm64=2.1.12-stable-10+b2 Downloading dependency 239 of 301: gettext-base:arm64=1.0-1 Downloading dependency 240 of 301: libcom-err2:arm64=1.47.4-1 Downloading dependency 241 of 301: libevent-pthreads-2.1-7t64:arm64=2.1.12-stable-10+b2 Downloading dependency 242 of 301: libgdbm6t64:arm64=1.26-1+b2 Downloading dependency 243 of 301: cmake:arm64=4.3.4-1 Downloading dependency 244 of 301: libncursesw6:arm64=6.6+20251231-1+b1 Downloading dependency 245 of 301: intltool-debian:arm64=0.35.0+20060710.6 Downloading dependency 246 of 301: libprrte-bin:arm64=3.0.13-3 Downloading dependency 247 of 301: libevent-openssl-2.1-7t64:arm64=2.1.12-stable-10+b2 Downloading dependency 248 of 301: libpython3.14:arm64=3.14.6-1 Downloading dependency 249 of 301: gcc-15-base:arm64=15.3.0-1 Downloading dependency 250 of 301: dh-python:arm64=7.20260623 Downloading dependency 251 of 301: libboost-dev:arm64=1.90.0.2 Downloading dependency 252 of 301: python3-mpi4py:arm64=4.1.2-1 Downloading dependency 253 of 301: libjs-jquery-ui:arm64=1.13.2+dfsg-1 Downloading dependency 254 of 301: libasan8:arm64=16.1.0-2 Downloading dependency 255 of 301: gcc-16-base:arm64=16.1.0-2 Downloading dependency 256 of 301: coreutils:arm64=9.10-1 Downloading dependency 257 of 301: debhelper:arm64=14.2Get:1 http://deb.debian.org/debian unstable/main arm64 debhelper all 14.2 [933 kB] Fetched 933 kB in 0s (72.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpop2xsa6u/debhelper_14.2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.14.6-1 [25.1 kB] Fetched 25.1 kB in 0s (2238 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi4g0es4b/python3_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.5.4-11 [168 kB] Fetched 168 kB in 0s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp581bgodz/libltdl-dev_2.5.4-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 util-linux arm64 2.42.2-1 [1184 kB] Fetched 1184 kB in 0s (40.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqzq2h9yn/util-linux_2.42.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (5635 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdhzol8to/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 9.1.1-1 [280 kB] Fetched 280 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdsakdtec/python3-pytest_9.1.1-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdebconfclient0 arm64 0.283 [7736 B] Fetched 7736 B in 0s (420 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq7zaqpbv/libdebconfclient0_0.283_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-ossl0 arm64 1.22.1-1 [21.6 kB] Fetched 21.6 kB in 0s (2134 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphw3srve4/libngtcp2-crypto-ossl0_1.22.1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.2.0-3 [295 kB] Fetched 295 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu1qda9a4/libbrotli1_1.2.0-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 5.0.10-1 [1029 kB] Fetched 1029 kB in 0s (39.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpka78uulv/libopenmpi-dev_5.0.10-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.22.1-3 [314 kB] Fetched 314 kB in 0s (24.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvw0crl87/libkrb5-3_1.22.1-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libstdc++-15-dev arm64 15.3.0-1 [2655 kB] Fetched 2655 kB in 0s (113 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp09b9e1_a/libstdc++-15-dev_15.3.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsystemd0 arm64 261.1-2 [425 kB] Fetched 425 kB in 0s (33.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8f3hgg7w/libsystemd0_261.1-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libubsan1 arm64 16.1.0-2 [1079 kB] Fetched 1079 kB in 0s (64.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfnlukowa/libubsan1_16.1.0-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libaudit1 arm64 1:4.1.2-1+b1 [59.7 kB] Fetched 59.7 kB in 0s (2384 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp9vl0r7w7/libaudit1_4.1.2-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.22.1-3 [74.7 kB] Fetched 74.7 kB in 0s (7153 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2v2k_9s1/libk5crypto3_1.22.1-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-3 [130 kB] Fetched 130 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyiacbd5f/libbsd0_0.12.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-tcti-cmd0t64 arm64 4.1.3-6 [33.8 kB] Fetched 33.8 kB in 0s (1419 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8u_jqe4i/libtss2-tcti-cmd0t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b2 [142 kB] Fetched 142 kB in 0s (6214 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeyfvgh7m/libxcb1_1.17.0-2+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 mawk arm64 1.3.4.20260302-1 [134 kB] Fetched 134 kB in 0s (6739 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppb_ruzq1/mawk_1.3.4.20260302-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.42.2-1 [98.4 kB] Fetched 98.4 kB in 0s (9201 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp63n86xbh/bsdextrautils_2.42.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libseccomp2 arm64 2.6.0-2+b1 [50.9 kB] Fetched 50.9 kB in 0s (3891 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphxs57w68/libseccomp2_2.6.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-9+b2 [867 kB] Fetched 867 kB in 0s (29.3 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmp8e87exyc/procps_4.0.4-9+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libibumad3 arm64 63.0-1.1+b3 [28.0 kB] Fetched 28.0 kB in 0s (2742 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpigu1wkkj/libibumad3_63.0-1.1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 26.2-2 [84.2 kB] Fetched 84.2 kB in 0s (4248 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5jij89fg/python3-packaging_26.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.4-1+b1 [42.0 kB] Fetched 42.0 kB in 0s (2156 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd6671uf5/ocl-icd-libopencl1_2.3.4-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260628T204121Z unstable/main arm64 libdrm-common all 2.4.134-2 [7840 B] Fetched 7840 B in 0s (421 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp478bnyrb/libdrm-common_2.4.134-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 6.0.0+really5.0.9-3+b2 [576 kB] Fetched 576 kB in 0s (39.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkx8g430i/libpmix2t64_6.0.0+really5.0.9-3+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3.14-minimal arm64 3.14.6-1 [2245 kB] Fetched 2245 kB in 0s (57.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf4hozi74/python3.14-minimal_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmount1 arm64 2.42.2-1 [200 kB] Fetched 200 kB in 0s (8080 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphomlejv2/libmount1_2.42.2-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-4 [234 kB] Fetched 234 kB in 0s (19.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnm809rec/libssh2-1t64_1.11.1-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-2+b1 [28.2 kB] Fetched 28.2 kB in 0s (1017 kB/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-2+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpus_f3gtm/libxdmcp6_1.1.5-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libzstd1 arm64 1.5.7+dfsg-3+b2 [257 kB] Fetched 257 kB in 0s (23.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq6_01q9k/libzstd1_1.5.7+dfsg-3+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpam-runtime all 1.7.0-6 [245 kB] Fetched 245 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbi8odq9o/libpam-runtime_1.7.0-6_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-4 [74.8 kB] Fetched 74.8 kB in 0s (3120 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr_dix0z5/readline-common_8.3-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.14.6-1 [25.1 kB] Fetched 25.1 kB in 0s (2470 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoiyjqbx2/python3-minimal_3.14.6-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtss2-tcti-mssim0t64 arm64 4.1.3-6 [35.3 kB] Fetched 35.3 kB in 0s (1831 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuyry9b2k/libtss2-tcti-mssim0t64_4.1.3-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 rpcsvc-proto arm64 1.4.4-1 [59.9 kB] Fetched 59.9 kB in 0s (3299 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6txovfhp/rpcsvc-proto_1.4.4-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.52.1-4 [151 kB] Fetched 151 kB in 0s (8102 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5h87e2xi/libuv1t64_1.52.1-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sysvinit-utils arm64 3.18-1 [29.6 kB] Fetched 29.6 kB in 0s (1422 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb7ray5c4/sysvinit-utils_3.18-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 xz-utils arm64 5.8.3-1 [738 kB] Fetched 738 kB in 0s (27.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiaxkst3u/xz-utils_5.8.3-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-11 [539 kB] Fetched 539 kB in 0s (20.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpykz0z42_/libtool_2.5.4-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Fetched 30.8 kB in 0s (1383 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp58_daz3i/media-types_14.0.0_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (9293 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw89q8gks/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 14.2 [77.1 kB] Fetched 77.1 kB in 0s (6370 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmfs4r8oj/libdebhelper-perl_14.2_all.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_arm64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmp5zbpol5o/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture arm64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.LF_MlDViSa as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.LF_MlDViSa 127.0.0.1 - - [29/Jun/2026 17:24:31] code 404, message File not found 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:42127 ./ InRelease 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:42127 ./ Release [462 B] 127.0.0.1 - - [29/Jun/2026 17:24:31] code 404, message File not found 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:42127 ./ Release.gpg 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:42127 ./ Packages [371 kB] Fetched 371 kB in 0s (9966 kB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./gcc-16-base_16.1.0-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libc-gconv-modules-extra_2.42-17_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libc6_2.42-17_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libgcc-s1_16.1.0-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./mawk_1.3.4.20260302-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./base-files_14.2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libtinfo6_6.6%2b20251231-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./debianutils_5.23.2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./bash_5.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libacl1_2.3.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libattr1_2.5.2-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libpcre2-8-0_10.46-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libselinux1_3.10-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libzstd1_1.5.7%2bdfsg-3%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./zlib1g_1.3.dfsg%2breally1.3.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libssl3t64_3.6.3-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./openssl-provider-legacy_3.6.3-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libsystemd0_261.1-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./coreutils_9.10-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./dash_0.5.12-12%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./diffutils_3.12-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libbz2-1.0_1.0.8-6%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./liblzma5_5.8.3-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libmd0_1.2.0-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./tar_1.35%2bdfsg-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./dpkg_1.23.7_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./findutils_4.10.0-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./grep_3.12-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./gzip_1.13-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./hostname_3.25%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./ncurses-bin_6.6%2b20251231-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:31] "GET /./libcrypt1_4.5.1-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./perl-base_5.40.1-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./sed_4.9-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libaudit-common_4.1.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libcap-ng0_0.9.3-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libaudit1_4.1.2-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libdb5.3t64_5.3.28%2bdfsg2-11%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./debconf_1.5.92_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libpam0g_1.7.0-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libpam-modules-bin_1.7.0-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libpam-modules_1.7.0-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libpam-runtime_1.7.0-6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libblkid1_2.42.2-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libmount1_2.42.2-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libsmartcols1_2.42.2-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libudev1_261.1-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libuuid1_2.42.2-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./util-linux_2.42.2-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libdebconfclient0_0.283_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./base-passwd_3.6.8%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./libc-bin_2.42-17_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./ncurses-base_6.6%2b20251231-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [29/Jun/2026 17:24:32] "GET /./sysvinit-utils_3.18-1_arm64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.LF_MlDViSa 127.0.0.1 - - [29/Jun/2026 17:24:35] code 404, message File not found 127.0.0.1 - - [29/Jun/2026 17:24:35] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:42127 ./ InRelease 127.0.0.1 - - [29/Jun/2026 17:24:35] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:42127 ./ Release 127.0.0.1 - - [29/Jun/2026 17:24:35] code 404, message File not found 127.0.0.1 - - [29/Jun/2026 17:24:35] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:42127 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... 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Building dependency tree... Reading state information... gcc-aarch64-linux-gnu is already the newest version (4:15.2.0-5+b1). gcc-aarch64-linux-gnu set to manually installed. base-files is already the newest version (14.2). perl-base is already the newest version (5.40.1-8). libhwloc15 is already the newest version (2.14.0-2). libhwloc15 set to manually installed. libatomic1 is already the newest version (16.1.0-2). libatomic1 set to manually installed. binutils is already the newest version (2.46.50.20260617-1). binutils set to manually installed. libibverbs-dev is already the newest version (63.0-1.1+b3). libibverbs-dev set to manually installed. libpsl5t64 is already the newest version (0.22.0-1). libpsl5t64 set to manually installed. liblapack3 is already the newest version (3.12.1-7+b2). liblapack3 set to manually installed. libpython3.14-dev is already the newest version (3.14.6-1). libpython3.14-dev set to manually installed. libblas-dev is already the newest version (3.12.1-7+b2). libblas-dev set to manually installed. bash is already the newest version (5.3-3). libtss2-sys1t64 is already the newest version (4.1.3-6). libtss2-sys1t64 set to manually installed. python3-dev is already the newest version (3.14.6-1). python3-dev set to manually installed. pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. gfortran-15 is already the newest version (15.3.0-1). gfortran-15 set to manually installed. liblzma5 is already the newest version (5.8.3-1). libhwloc-dev is already the newest version (2.14.0-2). libhwloc-dev set to manually installed. libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1+b1). mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. libmagic-mgc is already the newest version (1:5.47-4). libmagic-mgc set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.1-1). dh-strip-nondeterminism set to manually installed. libldap2 is already the newest version (2.6.13+dfsg-1). libldap2 set to manually installed. libudev1 is already the newest version (261.1-2). groff-base is already the newest version (1.24.1-1). groff-base set to manually installed. libtss2-rc0t64 is already the newest version (4.1.3-6). libtss2-rc0t64 set to manually installed. dash is already the newest version (0.5.12-12+b1). dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. autopoint is already the newest version (1.0-1). autopoint set to manually installed. file is already the newest version (1:5.47-4). file set to manually installed. libjs-sphinxdoc is already the newest version (9.1.0-4). libjs-sphinxdoc set to manually installed. libclang-common-21-dev is already the newest version (1:21.1.8-7+b3). libclang-common-21-dev set to manually installed. cpp-aarch64-linux-gnu is already the newest version (4:15.2.0-5+b1). cpp-aarch64-linux-gnu set to manually installed. libgfortran-15-dev is already the newest version (15.3.0-1). libgfortran-15-dev set to manually installed. make is already the newest version (4.4.1-3+b1). make set to manually installed. hostname is already the newest version (3.25+b1). libllvm21 is already the newest version (1:21.1.8-7+b3). libllvm21 set to manually installed. tpm-udev is already the newest version (4.1.3-6). tpm-udev set to manually installed. libcbor0.10 is already the newest version (0.10.2-2.1+b1). libcbor0.10 set to manually installed. python3.14 is already the newest version (3.14.6-1). python3.14 set to manually installed. systemd is already the newest version (261.1-2). systemd set to manually installed. ncurses-base is already the newest version (6.6+20251231-1). g++-aarch64-linux-gnu is already the newest version (4:15.2.0-5+b1). g++-aarch64-linux-gnu set to manually installed. libfftw3-bin is already the newest version (3.3.11-1). libfftw3-bin set to manually installed. libnl-3-dev is already the newest version (3.12.0-2+b1). libnl-3-dev set to manually installed. libtss2-esys-3.0.2-0t64 is already the newest version (4.1.3-6). libtss2-esys-3.0.2-0t64 set to manually installed. libucx0 is already the newest version (1.21.0-1). libucx0 set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b2). libnghttp2-14 is already the newest version (1.69.0-1). libnghttp2-14 set to manually installed. libelf1t64 is already the newest version (0.195-1). libelf1t64 set to manually installed. libgssapi-krb5-2 is already the newest version (1.22.1-3). libgssapi-krb5-2 set to manually installed. libnl-route-3-200 is already the newest version (3.12.0-2+b1). libnl-route-3-200 set to manually installed. mount is already the newest version (2.42.2-1). mount set to manually installed. libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. libffi8 is already the newest version (3.5.2-4). libffi8 set to manually installed. libc-dev-bin is already the newest version (2.42-17). libc-dev-bin set to manually installed. libtss2-tcti-device0t64 is already the newest version (4.1.3-6). libtss2-tcti-device0t64 set to manually installed. libpython3.14-stdlib is already the newest version (3.14.6-1). libpython3.14-stdlib set to manually installed. tar is already the newest version (1.35+dfsg-4). libmd0 is already the newest version (1.2.0-2). libperl5.40 is already the newest version (5.40.1-8). libperl5.40 set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). libevent-core-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-core-2.1-7t64 set to manually installed. gcc-15-aarch64-linux-gnu is already the newest version (15.3.0-1). gcc-15-aarch64-linux-gnu set to manually installed. libfftw3-double3 is already the newest version (3.3.11-1). libfftw3-double3 set to manually installed. libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b2). libattr1 is already the newest version (1:2.5.2-4). libprrte-dev is already the newest version (3.0.13-3). libprrte-dev set to manually installed. libpam0g is already the newest version (1.7.0-6). libuchardet0 is already the newest version (0.0.8-2+b2). libuchardet0 set to manually installed. bzip2 is already the newest version (1.0.8-6+b2). bzip2 set to manually installed. libdrm-amdgpu1 is already the newest version (2.4.134-2). libdrm-amdgpu1 set to manually installed. gfortran-15-aarch64-linux-gnu is already the newest version (15.3.0-1). gfortran-15-aarch64-linux-gnu set to manually installed. libsystemd-shared is already the newest version (261.1-2). libsystemd-shared set to manually installed. libngtcp2-16 is already the newest version (1.22.1-1). libngtcp2-16 set to manually installed. dwz is already the newest version (0.16-4). dwz set to manually installed. libkrb5support0 is already the newest version (1.22.1-3). libkrb5support0 set to manually installed. binutils-aarch64-linux-gnu is already the newest version (2.46.50.20260617-1). binutils-aarch64-linux-gnu set to manually installed. libpython3-stdlib is already the newest version (3.14.6-1). libpython3-stdlib set to manually installed. libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. libitm1 is already the newest version (16.1.0-2). libitm1 set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-8). perl-modules-5.40 set to manually installed. python3-numpy is already the newest version (1:2.4.6+ds-1). python3-numpy set to manually installed. gzip is already the newest version (1.13-1+b1). python3-numpy-dev is already the newest version (1:2.4.6+ds-1). python3-numpy-dev set to manually installed. libjansson4 is already the newest version (2.15.0-1). libjansson4 set to manually installed. liblsan0 is already the newest version (16.1.0-2). liblsan0 set to manually installed. libreadline8t64 is already the newest version (8.3-4). libreadline8t64 set to manually installed. python3-networkx is already the newest version (3.4.2-5). python3-networkx set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1+b1). binutils-common is already the newest version (2.46.50.20260617-1). binutils-common set to manually installed. libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. pybind11-dev is already the newest version (3.0.1-3). pybind11-dev set to manually installed. diffutils is already the newest version (1:3.12-1+b1). g++-15 is already the newest version (15.3.0-1). g++-15 set to manually installed. libarchive13t64 is already the newest version (3.8.7-1). libarchive13t64 set to manually installed. libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. libfuse3-4 is already the newest version (3.18.2-2). libfuse3-4 set to manually installed. libedit2 is already the newest version (3.1-20260512-1). libedit2 set to manually installed. findutils is already the newest version (4.10.0-4). libuuid1 is already the newest version (2.42.2-1). libibverbs1 is already the newest version (63.0-1.1+b3). libibverbs1 set to manually installed. base-passwd is already the newest version (3.6.8+b1). architecture-properties is already the newest version (0.2.6+b2). architecture-properties set to manually installed. init-system-helpers is already the newest version (1.69). libfftw3-single3 is already the newest version (3.3.11-1). libfftw3-single3 set to manually installed. libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. libproc2-0 is already the newest version (2:4.0.4-9+b2). libproc2-0 set to manually installed. libcurl4t64 is already the newest version (8.21.0-1). libcurl4t64 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. python3-pybind11 is already the newest version (3.0.1-3). python3-pybind11 set to manually installed. libgcc-s1 is already the newest version (16.1.0-2). libaudit-common is already the newest version (1:4.1.2-1). libucc1 is already the newest version (1.8.0-2). libucc1 set to manually installed. libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 set to manually installed. python3-iniconfig is already the newest version (2.1.0-2). python3-iniconfig set to manually installed. libdrm2 is already the newest version (2.4.134-2). libdrm2 set to manually installed. libselinux1 is already the newest version (3.10-1). libmuparser2v5 is already the newest version (2.3.4-2+b1). libmuparser2v5 set to manually installed. libfido2-1 is already the newest version (1.17.0-1). libfido2-1 set to manually installed. sed is already the newest version (4.9-3). libhwasan0 is already the newest version (16.1.0-2). libhwasan0 set to manually installed. libctf-nobfd0 is already the newest version (2.46.50.20260617-1). libctf-nobfd0 set to manually installed. libpam-modules is already the newest version (1.7.0-6). liblapack-dev is already the newest version (3.12.1-7+b2). liblapack-dev set to manually installed. libevent-dev is already the newest version (2.1.12-stable-10+b2). libevent-dev set to manually installed. libnl-3-200 is already the newest version (3.12.0-2+b1). libnl-3-200 set to manually installed. libc6-dev is already the newest version (2.42-17). libc6-dev set to manually installed. g++ is already the newest version (4:15.2.0-5+b1). g++ set to manually installed. ibverbs-providers is already the newest version (63.0-1.1+b3). ibverbs-providers set to manually installed. libexpat1 is already the newest version (2.8.2-1). libexpat1 set to manually installed. libexpat1-dev is already the newest version (2.8.2-1). libexpat1-dev set to manually installed. libgfortran5 is already the newest version (16.1.0-2). libgfortran5 set to manually installed. man-db is already the newest version (2.13.1-1+b1). man-db set to manually installed. grep is already the newest version (3.12-1+b1). libtsan2 is already the newest version (16.1.0-2). libtsan2 set to manually installed. libsmartcols1 is already the newest version (2.42.2-1). libltdl7 is already the newest version (2.5.4-11). libltdl7 set to manually installed. openssl-provider-legacy is already the newest version (3.6.3-1). pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. libssl3t64 is already the newest version (3.6.3-1). tzdata is already the newest version (2026b-1). tzdata set to manually installed. libjs-jquery is already the newest version (3.7.1+dfsg+~3.5.33-1). libjs-jquery set to manually installed. libgprofng0 is already the newest version (2.46.50.20260617-1). libgprofng0 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libstdc++6 is already the newest version (16.1.0-2). libstdc++6 set to manually installed. dpkg is already the newest version (1.23.7). libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. python3-pluggy is already the newest version (1.6.0-2). python3-pluggy set to manually installed. libnuma1 is already the newest version (2.0.19-1+b2). libnuma1 set to manually installed. libsframe3 is already the newest version (2.46.50.20260617-1). libsframe3 set to manually installed. python3.14-dev is already the newest version (3.14.6-1). python3.14-dev set to manually installed. libacl1 is already the newest version (2.3.2-3). patch is already the newest version (2.8-2+b1). patch set to manually installed. libpython3.14-minimal is already the newest version (3.14.6-1). libpython3.14-minimal set to manually installed. libcc1-0 is already the newest version (16.1.0-2). libcc1-0 set to manually installed. libz3-4 is already the newest version (4.13.3-1.1). libz3-4 set to manually installed. libmagic1t64 is already the newest version (1:5.47-4). libmagic1t64 set to manually installed. gcc is already the newest version (4:15.2.0-5+b1). gcc set to manually installed. libblas3 is already the newest version (3.12.1-7+b2). libblas3 set to manually installed. libnettle8t64 is already the newest version (3.10.2-1+b1). libnettle8t64 set to manually installed. librhash1 is already the newest version (1.4.6-1.1+b1). librhash1 set to manually installed. libibmad5 is already the newest version (63.0-1.1+b3). libibmad5 set to manually installed. liblz4-1 is already the newest version (1.10.0-10). liblz4-1 set to manually installed. autoconf is already the newest version (2.73-2). autoconf set to manually installed. libgomp1 is already the newest version (16.1.0-2). libgomp1 set to manually installed. libjsoncpp26 is already the newest version (1.9.7-4). libjsoncpp26 set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. libpython3-dev is already the newest version (3.14.6-1). libpython3-dev set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.1-1). libfile-stripnondeterminism-perl set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11+b1). libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. libpipeline1 is already the newest version (1.5.8-3). libpipeline1 set to manually installed. systemd-tpm is already the newest version (261.1-2). systemd-tpm set to manually installed. libbinutils is already the newest version (2.46.50.20260617-1). libbinutils set to manually installed. debianutils is already the newest version (5.23.2+b1). libkeyutils1 is already the newest version (1.6.3-6+b2). libkeyutils1 set to manually installed. libfftw3-long3 is already the newest version (3.3.11-1). libfftw3-long3 set to manually installed. librdmacm1t64 is already the newest version (63.0-1.1+b3). librdmacm1t64 set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b2). libxxhash0 set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. libgcc-15-dev is already the newest version (15.3.0-1). libgcc-15-dev set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b2). libgdbm-compat4t64 set to manually installed. libtss2-mu-4.0.1-0t64 is already the newest version (4.1.3-6). libtss2-mu-4.0.1-0t64 set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. openssh-client is already the newest version (1:10.3p1-5). openssh-client set to manually installed. gcc-15 is already the newest version (15.3.0-1). gcc-15 set to manually installed. libfabric1 is already the newest version (2.1.0-1.1+b2). libfabric1 set to manually installed. python3-pygments is already the newest version (2.19.2+dfsg-1). python3-pygments set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b2). libxau6 set to manually installed. libc6 is already the newest version (2.42-17). libc-bin is already the newest version (2.42-17). autotools-dev is already the newest version (20240727.1+nmu1). autotools-dev set to manually installed. libtss2-tcti-swtpm0t64 is already the newest version (4.1.3-6). libtss2-tcti-swtpm0t64 set to manually installed. libnl-route-3-dev is already the newest version (3.12.0-2+b1). libnl-route-3-dev set to manually installed. perl is already the newest version (5.40.1-8). perl set to manually installed. linux-libc-dev is already the newest version (7.0.13-1). linux-libc-dev set to manually installed. libpam-modules-bin is already the newest version (1.7.0-6). libblkid1 is already the newest version (2.42.2-1). libxml2-16 is already the newest version (2.15.3+dfsg-1). libxml2-16 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-17). libsqlite3-0 is already the newest version (3.53.3-1). libsqlite3-0 set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b2). libmuparser-dev is already the newest version (2.3.4-2+b1). libmuparser-dev set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. mpi-default-bin is already the newest version (1.20). mpi-default-bin set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1+b1). zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.2-3). zlib1g-dev set to manually installed. libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. libfftw3-dev is already the newest version (3.3.11-1). libfftw3-dev set to manually installed. bash-completion is already the newest version (1:2.16.0-8). bash-completion set to manually installed. libnuma-dev is already the newest version (2.0.19-1+b2). libnuma-dev set to manually installed. libhwloc-plugins is already the newest version (2.14.0-2). libhwloc-plugins set to manually installed. dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. g++-15-aarch64-linux-gnu is already the newest version (15.3.0-1). g++-15-aarch64-linux-gnu set to manually installed. cpp is already the newest version (4:15.2.0-5+b1). cpp set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-2.1-7t64 set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. automake is already the newest version (1:1.18.1-4). automake set to manually installed. cpp-15 is already the newest version (15.3.0-1). cpp-15 set to manually installed. libidn2-0 is already the newest version (2.3.8-5). libidn2-0 set to manually installed. libpciaccess0 is already the newest version (0.17-3+b4). libpciaccess0 set to manually installed. cpp-15-aarch64-linux-gnu is already the newest version (15.3.0-1). cpp-15-aarch64-linux-gnu set to manually installed. libctf0 is already the newest version (2.46.50.20260617-1). libctf0 set to manually installed. libcap-ng0 is already the newest version (0.9.3-1). gettext is already the newest version (1.0-1). gettext set to manually installed. libevent-extra-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-extra-2.1-7t64 set to manually installed. gettext-base is already the newest version (1.0-1). gettext-base set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-pthreads-2.1-7t64 set to manually installed. libgdbm6t64 is already the newest version (1.26-1+b2). libgdbm6t64 set to manually installed. cmake is already the newest version (4.3.4-1). cmake set to manually installed. libncursesw6 is already the newest version (6.6+20251231-1+b1). libncursesw6 set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libevent-openssl-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-openssl-2.1-7t64 set to manually installed. libpython3.14 is already the newest version (3.14.6-1). libpython3.14 set to manually installed. gcc-15-base is already the newest version (15.3.0-1). gcc-15-base set to manually installed. dh-python is already the newest version (7.20260623). dh-python set to manually installed. libboost-dev is already the newest version (1.90.0.2). libboost-dev set to manually installed. python3-mpi4py is already the newest version (4.1.2-1). python3-mpi4py set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libasan8 is already the newest version (16.1.0-2). libasan8 set to manually installed. gcc-16-base is already the newest version (16.1.0-2). coreutils 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(15.3.0-1). libstdc++-15-dev set to manually installed. libsystemd0 is already the newest version (261.1-2). libubsan1 is already the newest version (16.1.0-2). libubsan1 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libk5crypto3 is already the newest version (1.22.1-3). libk5crypto3 set to manually installed. libbsd0 is already the newest version (0.12.2-3). libbsd0 set to manually installed. libtss2-tcti-cmd0t64 is already the newest version (4.1.3-6). libtss2-tcti-cmd0t64 set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. mawk is already the newest version (1.3.4.20260302-1). bsdextrautils is already the newest version (2.42.2-1). bsdextrautils set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. procps is already the newest version (2:4.0.4-9+b2). procps set to manually installed. libibumad3 is already the newest version (63.0-1.1+b3). libibumad3 set to manually installed. python3-packaging is already the newest version (26.2-2). python3-packaging set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.4-1+b1). ocl-icd-libopencl1 set to manually installed. libdrm-common is already the newest version (2.4.134-2). libdrm-common set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3+b2). libpmix2t64 set to manually installed. python3.14-minimal is already the newest version (3.14.6-1). python3.14-minimal set to manually installed. libmount1 is already the newest version (2.42.2-1). libssh2-1t64 is already the newest version (1.11.1-4). libssh2-1t64 set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2+b1). libxdmcp6 set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b2). libpam-runtime is already the newest version (1.7.0-6). readline-common is already the newest version (8.3-4). readline-common set to manually installed. python3-minimal is already the newest version (3.14.6-1). python3-minimal set to manually installed. libtss2-tcti-mssim0t64 is already the newest version (4.1.3-6). libtss2-tcti-mssim0t64 set to manually installed. rpcsvc-proto is already the newest version (1.4.4-1). rpcsvc-proto set to manually installed. libuv1t64 is already the newest version (1.52.1-4). libuv1t64 set to manually installed. sysvinit-utils is already the newest version (3.18-1). xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. libtool is already the newest version (2.5.4-11). libtool set to manually installed. media-types is already the newest version (14.0.0). media-types set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libdebhelper-perl is already the newest version (14.2). libdebhelper-perl set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.LF_MlDViSa (Reading database ... 48367 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.LF_MlDViSa I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.LF_MlDViSa I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.LF_MlDViSa... I: success in 105.1498 seconds Downloading dependency 258 of 301: python3:arm64=3.14.6-1 Downloading dependency 259 of 301: libltdl-dev:arm64=2.5.4-11 Downloading dependency 260 of 301: util-linux:arm64=2.42.2-1 Downloading dependency 261 of 301: debconf:arm64=1.5.92 Downloading dependency 262 of 301: python3-pytest:arm64=9.1.1-1 Downloading dependency 263 of 301: libdebconfclient0:arm64=0.283 Downloading dependency 264 of 301: libngtcp2-crypto-ossl0:arm64=1.22.1-1 Downloading dependency 265 of 301: libbrotli1:arm64=1.2.0-3 Downloading dependency 266 of 301: libopenmpi-dev:arm64=5.0.10-1 Downloading dependency 267 of 301: libkrb5-3:arm64=1.22.1-3 Downloading dependency 268 of 301: libstdc++-15-dev:arm64=15.3.0-1 Downloading dependency 269 of 301: libsystemd0:arm64=261.1-2 Downloading dependency 270 of 301: libubsan1:arm64=16.1.0-2 Downloading dependency 271 of 301: libaudit1:arm64=1:4.1.2-1+b1 Downloading dependency 272 of 301: libk5crypto3:arm64=1.22.1-3 Downloading dependency 273 of 301: libbsd0:arm64=0.12.2-3 Downloading dependency 274 of 301: libtss2-tcti-cmd0t64:arm64=4.1.3-6 Downloading dependency 275 of 301: libxcb1:arm64=1.17.0-2+b2 Downloading dependency 276 of 301: mawk:arm64=1.3.4.20260302-1 Downloading dependency 277 of 301: bsdextrautils:arm64=2.42.2-1 Downloading dependency 278 of 301: libseccomp2:arm64=2.6.0-2+b1 Downloading dependency 279 of 301: procps:arm64=2:4.0.4-9+b2 Downloading dependency 280 of 301: libibumad3:arm64=63.0-1.1+b3 Downloading dependency 281 of 301: python3-packaging:arm64=26.2-2 Downloading dependency 282 of 301: ocl-icd-libopencl1:arm64=2.3.4-1+b1 Downloading dependency 283 of 301: libdrm-common:arm64=2.4.134-2 Downloading dependency 284 of 301: libpmix2t64:arm64=6.0.0+really5.0.9-3+b2 Downloading dependency 285 of 301: python3.14-minimal:arm64=3.14.6-1 Downloading dependency 286 of 301: libmount1:arm64=2.42.2-1 Downloading dependency 287 of 301: libssh2-1t64:arm64=1.11.1-4 Downloading dependency 288 of 301: libxdmcp6:arm64=1:1.1.5-2+b1 Downloading dependency 289 of 301: libzstd1:arm64=1.5.7+dfsg-3+b2 Downloading dependency 290 of 301: libpam-runtime:arm64=1.7.0-6 Downloading dependency 291 of 301: readline-common:arm64=8.3-4 Downloading dependency 292 of 301: python3-minimal:arm64=3.14.6-1 Downloading dependency 293 of 301: libtss2-tcti-mssim0t64:arm64=4.1.3-6 Downloading dependency 294 of 301: rpcsvc-proto:arm64=1.4.4-1 Downloading dependency 295 of 301: libuv1t64:arm64=1.52.1-4 Downloading dependency 296 of 301: sysvinit-utils:arm64=3.18-1 Downloading dependency 297 of 301: xz-utils:arm64=5.8.3-1 Downloading dependency 298 of 301: libtool:arm64=2.5.4-11 Downloading dependency 299 of 301: media-types:arm64=14.0.0 Downloading dependency 300 of 301: po-debconf:arm64=1.0.22 Downloading dependency 301 of 301: libdebhelper-perl:arm64=14.2 env --chdir=/srv/rebuilderd/tmp/rebuilderdVlvGFI/out DEB_BUILD_OPTIONS=parallel=8 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1782666441 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildHTjTXi/debrebuild.sbuildrc.r7tne4owU30t sbuild --build=arm64 --host=arm64 --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildHTjTXi/debrebuild.tar.EqvKBSecKecX --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --no-source --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=gromacs-2026.3 /srv/rebuilderd/tmp/rebuilderdVlvGFI/inputs/gromacs_2026.3-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on codethink02-arm64 +==============================================================================+ | gromacs 2026.3-1 (arm64) Mon, 29 Jun 2026 16:26:17 +0000 | +==============================================================================+ Package: gromacs Version: 2026.3-1 Source Version: 2026.3-1 Distribution: unstable Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildHTjTXi/debrebuild.tar.EqvKBSecKecX to /srv/rebuilderd/tmp/tmp.sbuild.oeAxjpXrXQ... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Mon, 29 Jun 2026 16:26:34 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdVlvGFI/inputs/gromacs_2026.3-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdVlvGFI/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 29 Jun 2026 16:26:38 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), make (>= 4.4), mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential Filtered Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), make (>= 4.4), mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-cyQFsK/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Mon, 29 Jun 2026 16:26:45 +0000 | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 29 Jun 2026 16:26:46 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.94+deb13-cloud-arm64 #1 SMP Debian 6.12.94-1 (2026-06-20) arm64 (aarch64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.0.13-1 Package versions: architecture-properties_0.2.6+b2 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-1 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8+b1 bash_5.3-3 bash-completion_1:2.16.0-8 binutils_2.46.50.20260617-1 binutils-aarch64-linux-gnu_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 cmake_4.3.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-aarch64-linux-gnu_15.3.0-1 cpp-aarch64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12+b1 debconf_1.5.92 debhelper_14.2 debianutils_5.23.2+b1 dh-autoreconf_22 dh-python_7.20260623 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1+b1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-aarch64-linux-gnu_15.3.0-1 g++-aarch64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-aarch64-linux-gnu_15.3.0-1 gcc-15-base_15.3.0-1 gcc-16-base_16.1.0-2 gcc-aarch64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-1 gettext-base_1.0-1 gfortran-15_15.3.0-1 gfortran-15-aarch64-linux-gnu_15.3.0-1 grep_3.12-1+b1 groff-base_1.24.1-1 gzip_1.13-1+b1 hostname_3.25+b1 ibverbs-providers_63.0-1.1+b3 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.7-1 libasan8_16.1.0-2 libatomic1_16.1.0-2 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblas-dev_3.12.1-7+b2 libblas3_3.12.1-7+b2 libblkid1_2.42.2-1 libboost-dev_1.90.0.2 libboost1.90-dev_1.90.0-6 libbrotli1_1.2.0-3 libbsd0_0.12.2-3 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1 libcbor0.10_0.10.2-2.1+b1 libcc1-0_16.1.0-2 libclang-common-21-dev_1:21.1.8-7+b3 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl4t64_8.21.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.2 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.134-2 libdrm-common_2.4.134-2 libdrm2_2.4.134-2 libedit2_3.1-20260512-1 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libevent-core-2.1-7t64_2.1.12-stable-10+b2 libevent-dev_2.1.12-stable-10+b2 libevent-extra-2.1-7t64_2.1.12-stable-10+b2 libevent-openssl-2.1-7t64_2.1.12-stable-10+b2 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2 libexpat1_2.8.2-1 libexpat1-dev_2.8.2-1 libfabric1_2.1.0-1.1+b2 libffi8_3.5.2-4 libfftw3-bin_3.3.11-1 libfftw3-dev_3.3.11-1 libfftw3-double3_3.3.11-1 libfftw3-long3_3.3.11-1 libfftw3-single3_3.3.11-1 libfido2-1_1.17.0-1 libfile-stripnondeterminism-perl_1.15.1-1 libfuse3-4_3.18.2-2 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-15-dev_15.3.0-1 libgfortran5_16.1.0-2 libgmp10_2:6.3.0+dfsg-5+b2 libgomp1_16.1.0-2 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16.1.0-2 libhwloc-dev_2.14.0-2 libhwloc-plugins_2.14.0-2 libhwloc15_2.14.0-2 libibmad5_63.0-1.1+b3 libibumad3_63.0-1.1+b3 libibverbs-dev_63.0-1.1+b3 libibverbs1_63.0-1.1+b3 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.0-1 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_9.1.0-4 libjsoncpp26_1.9.7-4 libk5crypto3_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5support0_1.22.1-3 liblapack-dev_3.12.1-7+b2 liblapack3_3.12.1-7+b2 libldap2_2.6.13+dfsg-1 libllvm21_1:21.1.8-7+b3 liblsan0_16.1.0-2 libltdl-dev_2.5.4-11 libltdl7_2.5.4-11 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libmuparser-dev_2.3.4-2+b1 libmuparser2v5_2.3.4-2+b1 libncursesw6_6.6+20251231-1+b1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp3-9_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-ossl0_1.22.1-1 libnl-3-200_3.12.0-2+b1 libnl-3-dev_3.12.0-2+b1 libnl-route-3-200_3.12.0-2+b1 libnl-route-3-dev_3.12.0-2+b1 libnuma-dev_2.0.19-1+b2 libnuma1_2.0.19-1+b2 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libpam-modules_1.7.0-6 libpam-modules-bin_1.7.0-6 libpam-runtime_1.7.0-6 libpam0g_1.7.0-6 libpciaccess0_0.17-3+b4 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpmix2t64_6.0.0+really5.0.9-3+b2 libproc2-0_2:4.0.4-9+b2 libprrte-bin_3.0.13-3 libprrte-dev_3.0.13-3 libprrte3_3.0.13-3 libpsl5t64_0.22.0-1 libpython3-dev_3.14.6-1 libpython3-stdlib_3.14.6-1 libpython3.14_3.14.6-1 libpython3.14-dev_3.14.6-1 libpython3.14-minimal_3.14.6-1 libpython3.14-stdlib_3.14.6-1 librdmacm1t64_63.0-1.1+b3 libreadline8t64_8.3-4 librhash1_1.4.6-1.1+b1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssh2-1t64_1.11.1-4 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd-shared_261.1-2 libsystemd0_261.1-2 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16.1.0-2 libtss2-esys-3.0.2-0t64_4.1.3-6 libtss2-mu-4.0.1-0t64_4.1.3-6 libtss2-rc0t64_4.1.3-6 libtss2-sys1t64_4.1.3-6 libtss2-tcti-cmd0t64_4.1.3-6 libtss2-tcti-device0t64_4.1.3-6 libtss2-tcti-mssim0t64_4.1.3-6 libtss2-tcti-swtpm0t64_4.1.3-6 libubsan1_16.1.0-2 libucc1_1.8.0-2 libuchardet0_0.0.8-2+b2 libucx0_1.21.0-1 libudev1_261.1-2 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libuv1t64_1.52.1-4 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2+b1 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.3+dfsg-1 libxnvctrl0_535.171.04-1+b3 libxxhash0_0.8.3-2+b2 libz3-4_4.13.3-1.1 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.0.13-1 m4_1.4.21-1 make_4.4.1-3+b1 man-db_2.13.1-1+b1 mawk_1.3.4.20260302-1 media-types_14.0.0 mount_2.42.2-1 mpi-default-bin_1.20 mpi-default-dev_1.20 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1+b1 netbase_6.5 ocl-icd-libopencl1_2.3.4-1+b1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.3p1-5 openssl-provider-legacy_3.6.3-1 patch_2.8-2+b1 perl_5.40.1-8 perl-base_5.40.1-8 perl-modules-5.40_5.40.1-8 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 procps_2:4.0.4-9+b2 pybind11-dev_3.0.1-3 python3_3.14.6-1 python3-dev_3.14.6-1 python3-iniconfig_2.1.0-2 python3-minimal_3.14.6-1 python3-mpi4py_4.1.2-1 python3-networkx_3.4.2-5 python3-numpy_1:2.4.6+ds-1 python3-numpy-dev_1:2.4.6+ds-1 python3-packaging_26.2-2 python3-pluggy_1.6.0-2 python3-pybind11_3.0.1-3 python3-pygments_2.19.2+dfsg-1 python3-pytest_9.1.1-1 python3.14_3.14.6-1 python3.14-dev_3.14.6-1 python3.14-minimal_3.14.6-1 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sed_4.9-3 sensible-utils_0.0.26 systemd_261.1-2 systemd-tpm_261.1-2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tpm-udev_4.1.3-6 tzdata_2026b-1 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Mon, 29 Jun 2026 16:26:46 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gromacs Binary: gromacs, gromacs-data, libgromacs11, libgromacs-dev, libnblib-gmx0, libnblib-gmx-dev Architecture: any all Version: 2026.3-1 Maintainer: Debichem Team Uploaders: Nicholas Breen Homepage: https://www.gromacs.org/ Standards-Version: 4.7.4 Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, mpi-default-bin, perl Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), make (>= 4.4), mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev Build-Depends-Indep: doxygen, furo, ghostscript, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended Package-List: gromacs deb science optional arch=any gromacs-data deb science optional arch=all libgromacs-dev deb libdevel optional arch=any libgromacs11 deb libs optional arch=any libnblib-gmx-dev deb libdevel optional arch=any libnblib-gmx0 deb libs optional arch=any Checksums-Sha1: 1cb152d8a66c3fb2a651e433c11df869449f7c87 16580747 gromacs_2026.3.orig-regressiontests.tar.gz 36d3783da04349263f4143ff5bac6ce2a1ec0190 45914529 gromacs_2026.3.orig.tar.gz 0b8e58721482330d3c8a3b5e619c36482073fb9f 13665824 gromacs_2026.3-1.debian.tar.xz Checksums-Sha256: ec28a220729e8ad5e2a668919d201b3f283d37ecd3d6e7aa0f7c8a2fa278fa6a 16580747 gromacs_2026.3.orig-regressiontests.tar.gz 1094b7bbc6a3960223827114626657110b40096cdf9598a727935fc84ebf8aa0 45914529 gromacs_2026.3.orig.tar.gz 79054d93c2874a4cbcd727aad89d9dcfc8d4aec26a03e7b129a59d7a4d938861 13665824 gromacs_2026.3-1.debian.tar.xz Files: 2efca4799115329160ccaf84ce442baf 16580747 gromacs_2026.3.orig-regressiontests.tar.gz 7987af0c6ab939ab6e639f32d0dd260f 45914529 gromacs_2026.3.orig.tar.gz 2eabb7c3c16f17ee0c4aed543f2ce990 13665824 gromacs_2026.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmpBVVASHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCPyZwP/js+dNgpLnIExuv6yB8Te7UooeXAvwiV MsG1Fg4u7rk/hHwrlvRP0ABQnjW53bNT1RDMt1Mn8XciFzmiQoWvpCJgaRs3UbJO XCI0BO5pVcJZS37iz8mqjxdJpxIGXpoAntMF6Jcp6jb0PS5sXWwy3ghXPEIft79B 9BGLNLnou1VVvQeQLwBj4ZgkySbFY88YCfAG1UBOa+NnAlV84AXXOmipnW7EsqQj mi2YqdpV7tFc301ev3uAhhYIjl/noMaMFh+J650tkbkQ3YuxiwnVxNSV6Gy7nF93 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/build/reproducible-path/gromacs-2026.3 dpkg-source: info: unpacking gromacs_2026.3.orig.tar.gz dpkg-source: info: unpacking gromacs_2026.3.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2026.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying script-shebang-line.patch dpkg-source: info: applying threadmpi-tests.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1782666441 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2026.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary-arch dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2026.3 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.14.6", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.11 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (34.6s) -- Generating done (1.7s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.3/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2026.3 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.14.6", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.11 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (31.8s) -- Generating done (1.6s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.3/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2026.3 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.14.6", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.10 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.11 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO_AUTO -- Performing Test HAS_FLTO_AUTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2026.3/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "3.0.1") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) Doxygen needs to be installed to generate the C++ documentation -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (34.6s) -- Generating done (1.9s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.3/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2026.3 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.14.6", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.10 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.11 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (34.3s) -- Generating done (1.1s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.3/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j8 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.3 -B/build/reproducible-path/gromacs-2026.3/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.3/build/basic/CMakeFiles /build/reproducible-path/gromacs-2026.3/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/selection /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.3/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.3-Debian_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.3/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.3/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-1 -P /build/reproducible-path/gromacs-2026.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/parser.cpp /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include 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-DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvar.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmm_mdmodule.cpp [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/binary_information.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include 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/build/reproducible-path/gromacs-2026.3/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/alltoall.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmforceproviderbuilder.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 1%] Built target linearalgebra /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md/h5md.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmoptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 1%] Built target scanner cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 5%] Built target thread_mpi /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/abstractsection.cpp [ 5%] Built target h5md /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/xtc3.c /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 5%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/filenameoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 6%] Built target fmm cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/filenameoptionmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 6%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsassigner.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 6%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/treesupport.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 8%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_meta.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 8%] Built target pulling cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/decidegpuusage.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 10%] Built target options cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong 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"--color=" modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_protein.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 10%] Built target taskassignment cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.3/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrun/tpi.cpp: In member function ‘std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)’: /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrun/tpi.cpp:497:85: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 497 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/printtime.cpp cd 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/particletype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/template.dir/link.d CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 95%] Built target template cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include 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api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include 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/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS 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CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/samples /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" argon-forces-integration make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/samples /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/samples/methane-water-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.3/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/bwt.c cd 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/p2p_wait.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/collective.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/dict.c cd 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/comm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/huffman.c /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/binary_information.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/abstractoption.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/mtf.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 0%] Built target h5md /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmforceproviderbuilder.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/numa_malloc.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 1%] Built target thread_mpi cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvaratoms.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 3%] Built target fmm /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/filenameoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 5%] Built target linearalgebra /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 5%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 5%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_histogram.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/treesupport.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pull_rotation.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 8%] Built target options cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/findallgputasks.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator/checkpointhelper.cpp cd 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include 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CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 12%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 13%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.3/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.3/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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/build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c 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/build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem 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/build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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/build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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/build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/benchmark/bench_system.cpp cd 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include 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-isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_manager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/nvshmem_manager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrun/tpi.cpp: In member function ‘std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)’: /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrun/tpi.cpp:497:85: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 497 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/plainpairlistranges.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/print_validation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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&& /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.3/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.3/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-soname,libgromacs_d.so.11 -o ../../lib/libgromacs_d.so.11.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.11.0.0 ../../lib/libgromacs_d.so.11 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 94%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/gmxapi /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" nblib /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/resourceassignment.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/exceptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/molecules.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 94%] Built target gmx cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include 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/build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include 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CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp 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CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/samples /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" methane-water-integration make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/samples /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" argon-forces-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/samples/methane-water-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.3/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.3/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.3/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -j8 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.3 -B/build/reproducible-path/gromacs-2026.3/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.3 -B/build/reproducible-path/gromacs-2026.3/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.3/build/basic/CMakeFiles 95 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.3/build/basic/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" gtest make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/selection /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.3/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs 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-std=c++17 -fPIC -Wall -Wshadow -Wundef -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-declarations -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.3-Debian_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.3/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.3/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-1 -P /build/reproducible-path/gromacs-2026.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Entering directory 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src/gromacs/fmm/CMakeFiles/fmm.dir/depend [ 1%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd 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linearalgebra [ 1%] Built target lmfit_objlib [ 1%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 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directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'src/gromacs/fmm/CMakeFiles/fmm.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 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src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 4%] Built target h5md [ 5%] Built target fmm /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/depend /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test 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make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/DependInfo.cmake "--color=" alloc_check make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make 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/usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -MF CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o.d -o CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/sync_cyclecount.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build [ 7%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build.make src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -MF CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/mpi_speedtest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/alloc_check.cpp.o -MF CMakeFiles/alloc_check.dir/alloc_check.cpp.o.d -o CMakeFiles/alloc_check.dir/alloc_check.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/alloc_check.cpp [ 8%] Built target options /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/reduce.cpp.o -MF CMakeFiles/mpithreads.dir/reduce.cpp.o.d -o CMakeFiles/mpithreads.dir/reduce.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/reduce.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 8%] Built target pulling /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -MF CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/send_recv.cpp [ 8%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -MF CMakeFiles/mpi_speedtest.dir/multicast.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/alloc_check.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/sync_cyclecount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alloc_check.dir/link.d CMakeFiles/alloc_check.dir/alloc_check.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/alloc_check make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/once.cpp.o -MF CMakeFiles/mpithreads.dir/once.cpp.o.d -o CMakeFiles/mpithreads.dir/once.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/once.cpp [ 8%] Built target alloc_check /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sync_cyclecount.dir/link.d CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/sync_cyclecount make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 8%] Built target sync_cyclecount cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/send_recv.cpp.o -MF CMakeFiles/mpithreads.dir/send_recv.cpp.o.d -o CMakeFiles/mpithreads.dir/send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/send_recv.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 8%] Built target taskassignment /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/multicast.cpp.o -MF CMakeFiles/mpithreads.dir/multicast.cpp.o.d -o CMakeFiles/mpithreads.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cond-var.cpp.o -MF CMakeFiles/mpithreads.dir/cond-var.cpp.o.d -o CMakeFiles/mpithreads.dir/cond-var.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/cond-var.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 9%] Built target modularsimulator cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/atomic.cpp.o -MF CMakeFiles/mpithreads.dir/atomic.cpp.o.d -o CMakeFiles/mpithreads.dir/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/atomic.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cycles.cpp.o -MF CMakeFiles/mpithreads.dir/cycles.cpp.o.d -o CMakeFiles/mpithreads.dir/cycles.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/cycles.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/split.cpp.o -MF CMakeFiles/mpithreads.dir/split.cpp.o.d -o CMakeFiles/mpithreads.dir/split.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/split.cpp /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/notmpi.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpi_speedtest.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpithreads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpi_speedtest.dir/link.d CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpi_speedtest make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 9%] Built target mpi_speedtest /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpithreads.dir/link.d CMakeFiles/mpithreads.dir/main.cpp.o CMakeFiles/mpithreads.dir/reduce.cpp.o CMakeFiles/mpithreads.dir/once.cpp.o CMakeFiles/mpithreads.dir/send_recv.cpp.o CMakeFiles/mpithreads.dir/multicast.cpp.o "CMakeFiles/mpithreads.dir/cond-var.cpp.o" CMakeFiles/mpithreads.dir/atomic.cpp.o CMakeFiles/mpithreads.dir/cycles.cpp.o CMakeFiles/mpithreads.dir/split.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o 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/build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/gmxapi /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" nblib make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 61%] Built target gmxapi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 62%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/tests/mpitest.cpp /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/calcvir.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 64%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o" "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 64%] Built target utility-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpicomm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpicomm-test.dir/link.d "CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o" "CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mpicomm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 64%] Built target mpicomm-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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CMakeFiles/testutils-test.dir/posixmemstream.cpp.o.d -o CMakeFiles/testutils-test.dir/posixmemstream.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/tests/posixmemstream.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -MF CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o.d -o CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constraintgroupsize.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 64%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" 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-I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" 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-DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" density_fitting_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/posixmemstream.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 65%] Built target testutils-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 66%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" qmmm_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/biasstate.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" colvars_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" plumed_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 66%] Built target density_fitting_applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmforceproviderstate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" plumed_md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 66%] Built target plumed_applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 67%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 68%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" nnpot_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/logger.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 68%] Built target awh-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 69%] Built target plumed_md-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" listed_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF 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Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 69%] Built target applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mpicomm.cpp.o -MF CMakeFiles/utility-test.dir/mpicomm.cpp.o.d -o CMakeFiles/utility-test.dir/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" nbnxm-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/path.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" nbnxm-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 70%] Built target nbnxm-gpu-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" nonbonded-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/kernelsetup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 70%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 70%] Built target nnpot_applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -MF CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o.d -o CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/plainpairlist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include 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-isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/simulationsignal.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/DependInfo.cmake "--color=" nonbonded-fep-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/freeenergygpukernel.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/testsystem.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/testsystem.cpp: In function ‘std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)’: /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-gpu-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/template_mp.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" onlinehelp-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests/mock_helptopic.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-gpu-test.dir/link.d "CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o" "CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 71%] Built target nonbonded-fep-gpu-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/vsite.cpp.o -MF CMakeFiles/mdlib-test.dir/vsite.cpp.o.d -o CMakeFiles/mdlib-test.dir/vsite.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/vsite.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 71%] Built target nbnxm-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" domdec-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem 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-o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" domdec-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 71%] Built target onlinehelp-test-shared cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 71%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" ewald-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests/localatomsetmanager.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 71%] Built target domdec-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/DependInfo.cmake "--color=" fmm-interface-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 71%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmesolvetest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/vsite.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/txtdump.cpp.o -MF CMakeFiles/utility-test.dir/txtdump.cpp.o.d -o CMakeFiles/utility-test.dir/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/txtdump.cpp [ 73%] Built target mdlib-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 73%] Built target fft-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests/fmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests/fmmforceproviderbuilder.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include 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-DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/typecasts.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem 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/usr/bin/cmake -E cmake_link_script CMakeFiles/fmm-interface-tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fmm-interface-tests.dir/link.d "CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o" "CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fmm-interface-tests ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 73%] Built target fmm-interface-tests cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make 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src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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/build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/arrayrefwithpadding.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/mpicomm.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/txtdump.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/vecdump.cpp.o" "CMakeFiles/utility-test.dir/vectypes.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 75%] Built target utility-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests/device_management.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 75%] Built target ewald-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-mpi-test.dir/link.d "CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o" "CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 76%] Built target gpu_utils-mpi-test cd 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/build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory 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src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 76%] Built target hardware-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 76%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 77%] Built target mdspan-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/tests/mshift.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 77%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd 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/build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/densityfittingforce.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/tests/multipletimestepping.cpp /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/DependInfo.cmake "--color=" serialization-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/tests/keyvaluetreeserializer.cpp /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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CMakeFiles/random-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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"CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target random-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include 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-I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/optimization.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target mdtypes-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/serialization-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/serialization-test.dir/link.d "CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/serialization-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/repeatingsection.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target serialization-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/treesupport.cpp /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" timing-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/base.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target taskassignment-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/bootstrap_loadstore.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/entropy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target table-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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-isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -MF CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmxanatestbase.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ 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-isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/generate_test_points.cpp.o -MF CMakeFiles/simd-test.dir/generate_test_points.cpp.o.d -o CMakeFiles/simd-test.dir/generate_test_points.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/generate_test_points.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/scalar.cpp /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/generate_test_points.cpp: In function ‘std::vector gmx::test::generateTestPoints(RealRange, std::size_t)’: /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/generate_test_points.cpp:53:19: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 53 | std::vector generateTestPoints(RealRange inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/compat/tests/pointers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target pull-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target compat-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/editconf.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_traj.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 78%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 80%] Built target math-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/genrestr.cpp /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" correlations-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/correlationfunctions/tests/autocorr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 80%] Built target options-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 81%] Built target gmxana-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/correlationfunctions/tests/expfit.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 81%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" analysisdata-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include 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CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 82%] Built target topology-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: 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'/build/reproducible-path/gromacs-2026.3/build/basic' [ 82%] Built target correlations-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 82%] Built target pdb2gmx3-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/legacyenergy.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" tool-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_math.cpp: In static member function ‘static void gmx::test::SimdMathTest::generateTestPointsTest()’: /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_math.cpp:309:32: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 309 | result = generateTestPoints({ -1e10, -1 }, points); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" tool-test-with-leaks make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 83%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/DependInfo.cmake "--color=" h5md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o -MF CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o.d -o CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md/tests/h5md_disabled.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 83%] Built target analysisdata-test-shared cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/h5md-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/h5md-test.dir/link.d "CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o" "CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/h5md.dir/h5md.cpp.o -o ../../../../../bin/h5md-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 84%] Built target h5md-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 84%] Built target tool-test-with-leaks cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/generate_test_points.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 86%] Built target simd-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF 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'/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/solvate.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 86%] Built target tool-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/filetypes.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/settimestep.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 87%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/trajectory_writing.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 87%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 88%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 88%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/toputils.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/awh.cpp.o -MF CMakeFiles/mdrun-test.dir/awh.cpp.o.d -o CMakeFiles/mdrun-test.dir/awh.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/awh.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/multiple_time_stepping.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" mdrun-single-rank-algorithms-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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-isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" minimize-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 88%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/swapcoords.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 88%] Built target mdrun-single-rank-algorithms-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/tngio.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/boxdeformation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -MF CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o.d -o CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/xdr_serializer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 88%] Built target selection-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 88%] Built target minimize-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/simple_mdrun.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" mdrun-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 88%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" mdrun-multisim-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/multisim.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/awh.cpp.o" "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 89%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-equivalence-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY 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'/build/reproducible-path/gromacs-2026.3/build/basic' [ 90%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" mdrun-mpi-pme-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 90%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" mdrun-coordination-basic-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 91%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" mdrun-coordination-coupling-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" mdrun-coordination-constraints-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 91%] Built target mdrun-multisim-replex-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 91%] Built target mdrun-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions_constraints.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 92%] Built target mdrun-mpi-pme-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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-MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/expandedensemble.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" mdrun-pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 92%] Built target mdrun-coordination-basic-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/pull_rotation.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" mdrun-simulator-comparison-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 93%] Built target mdrun-coordination-coupling-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" mdrun-vsites-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/virtualsites.cpp cd 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 93%] Built target mdrun-multisim-replex-equivalence-test cd 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Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 94%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" nblib-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/integrator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 94%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 94%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" nblib-setup-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 95%] Built target workflow-details-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include 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-isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" nblib-tpr-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 95%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" nblib-integration-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests 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-isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" nblib-listed-forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/nbkernelsystem.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include 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api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 96%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/molecules.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 96%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/nbnxmsetup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 96%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 96%] Built target gmxapi-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/util/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" nblib-util-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/simstate.cpp /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 96%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include 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api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/filenm.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -MF CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/plainpairlistranges.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 97%] Built target nblib-setup-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && 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/build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 97%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/angle.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 98%] Built target commandline-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" nblib-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 98%] Built target nblib-tests cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [ 98%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' cd /build/reproducible-path/gromacs-2026.3/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic /build/reproducible-path/gromacs-2026.3/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.3/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.3/build/basic/lib ctest -V ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2026.3/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2026.3/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2026.3/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -536878113 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.024 0.012 199.1 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 42.661 0.563 3.956 0.002 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (264 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -71320321 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.010 0.005 197.9 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 100.930 0.238 1.672 0.005 1: [ OK ] GmxApiTest.RunnerBasicMD (171 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to 1775695597 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.100 0.050 199.8 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 70.551 0.340 2.392 0.003 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.107 0.054 199.8 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 66.042 0.363 2.555 0.003 1: [ OK ] GmxApiTest.RunnerReinitialize (278 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -822240771 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.015 0.008 198.4 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 66.766 0.359 2.527 0.003 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: NOTE: 11 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.054 0.027 199.6 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 18.747 1.280 9.001 0.001 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (207 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -1158295706 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.015 0.007 198.6 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 115.384 0.208 1.463 0.005 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.3-Debian_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.011 0.006 192.8 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 60.079 0.399 2.809 0.003 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (184 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to 1805626335 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (154 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (1262 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (1298 ms total) 1: [ PASSED ] 9 tests. 1/104 Test #1: GmxapiExternalInterfaceTests .............. Passed 1.40 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -3245313 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (158 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 1053289398 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (144 ms) 2: [----------] 2 tests from GmxApiTest (303 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (311 ms total) 2: [ PASSED ] 2 tests. 2/104 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.33 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (1 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (11 ms) 3: [----------] 8 tests from NBlibTest (15 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (1 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (4 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (2 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (2 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (8 ms) 3: [----------] 1 test from LinearChainDataFixture (8 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (35 ms total) 3: [ PASSED ] 44 tests. 3/104 Test #3: NbLibListedForcesTests .................... Passed 0.05 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/104 Test #4: NbLibSamplesTestArgon ..................... Passed 0.03 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 5/104 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.02 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 60 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (1 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (1 ms total) 6: [ PASSED ] 16 tests. 6/104 Test #6: NbLibUtilTests ............................ Passed 0.02 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (3 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (4 ms total) 7: [ PASSED ] 57 tests. 7/104 Test #7: NbLibSetupTests ........................... Passed 0.03 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests 8: Test timeout computed to be: 60 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2026.3-Debian_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (15 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2026.3-Debian_1 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (12 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2026.3-Debian_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (14 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (12 ms) 8: [----------] 4 tests from TprReaderTest (56 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (70 ms total) 8: [ PASSED ] 4 tests. 8/104 Test #8: NbLibTprTests ............................. Passed 0.10 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (1 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (9 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (9 ms total) 9: [ PASSED ] 20 tests. 9/104 Test #9: NbLibIntegrationTests ..................... Passed 0.03 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/104 Test #10: NbLibIntegratorTests ...................... Passed 0.02 sec test 11 Start 11: threadMPI-mpithreads 11: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mpithreads "-nt" "3" 11: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test 11: Test timeout computed to be: 1500 11: 11: thread_mpi tester. 11: 11: Number of threads: 3 11: 11: thread 0: got arg 10; total number of hw threads: 12 11: my rank = 0 11: Setting thread affinity 11: thread 1: got arg 10; total number of hw threads: 12 11: my rank = 1 11: thread 2: got arg 10; total number of hw threads: 12 11: my rank = 2 11: Testing atomic functions.. 11: OK. 11: Starting tMPI_Thread_cond_signal test: 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 1: 104 11: processed by thread 2: 896 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 2 11: processed by thread 2: 998 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 671 11: processed by thread 1: 329 11: 11: Starting tMPI_Thread_cond_broadcast test: 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 1: 1698 11: processed by thread 2: 302 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 850 11: processed by thread 2: 1150 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 825 11: processed by thread 1: 1175 11: 11: 11: sizeof(atomic_t) = 4, sizeof(atomic_t_ptr)=8, sizeof(spinlock)=4 11: Testing spinlocks.. 11: OK. 11: 11: Testing locks.. 11: OK. 11: 11: Barrier data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Starting MPI_Send and MPI_Recv tests 11: Received: 'From thread 2 to 0: hello.' 11: Received: 'From thread 1 to 0: hello.' 11: Received: 'From thread 2 to 1: hello.' 11: Received: 'From thread 1 to 1: hello.' 11: 11: Starting MPI_Sendrecv tests 11: Received: 'Sendrecv hello, from thread 1' 11: Received: 'Sendrecv hello, from thread 2' 11: Received: 'Sendrecv hello, from thread 0' 11: 11: Starting MPI_Isend/MPI_Irecv tests 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0xffff90005b90 of size 2 11: I'm in world rank 0, and have new rank 1 in group 0xffff90005b90 of size 2 11: 11: Starting MPI_Split test 11: I'm in world rank 1, and have new rank 0 in group 0xffff90006150 of size 1 11: I'm in world rank 2, and have new rank 0 in group 0xffff90006b60 of size 1 11: my rank is 2, MPI_Comm_compare said: 3 11: I'm in world rank 1, and have new rank 0 in group 0xffff90006820 of size 1 11: my rank is 1, MPI_Comm_compare said: 3 11: I'm in world rank 0, and have new rank 0 in group 0xffff900065a0 of size 1 11: my rank is 0, MPI_Comm_compare said: 3 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0xffff90006b60 of size 3 11: I'm in world rank 1, and have new rank 1 in group 0xffff90006b60 of size 3 11: my rank is 2, MPI_Comm_compare said: 2 11: my rank is 1, MPI_Comm_compare said: 2 11: I'm in world rank 0, and have new rank 2 in group 0xffff90006b60 of size 3 11: my rank is 0, MPI_Comm_compare said: 2 11: Starting repeated MPI_Split() test. 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: Done. 11: 11: Starting MPI_Bcast test 11: Received: 'Broadcast message 0 from 0' 11: Received: 'Broadcast message 0 from 1' 11: Received: 'Broadcast message 0 from 2' 11: Received: 'Broadcast message 1 from 0' 11: Received: 'Broadcast message 1 from 1' 11: Received: 'Broadcast message 1 from 2' 11: Broadcast data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Gather test 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Gather data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Gatherv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Scatter test 11: Received from 0: 'Scatter message from 000 to 000' 11: Received back from 1: 'Scatter message from 000 to 001' 11: Received back from 2: 'Scatter message from 000 to 002' 11: Scatter data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Scatterv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Alltoall test 11: From 0: 0->0(0) 1->0(0) 2->0(0) 11: From 1: 0->1(0) 1->1(0) 2->1(0) 11: From 2: 0->2(0) 1->2(0) 2->2(0) 11: From 0: 0->0(1) 1->0(1) 2->0(1) 11: From 1: 0->1(1) 1->1(1) 2->1(1) 11: From 2: 0->2(1) 1->2(1) 2->2(1) 11: From 0: 0->0(2) 1->0(2) 2->0(2) 11: From 1: 0->1(2) 1->1(2) 2->1(2) 11: From 2: 0->2(2) 1->2(2) 2->2(2) 11: From 0: 0->0(3) 1->0(3) 2->0(3) 11: From 1: 0->1(3) 1->1(3) 2->1(3) 11: From 2: 0->2(3) 1->2(3) 2->2(3) 11: Alltoallv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Reduce test 11: Results from mpi_reduce: 11: again: my rank = 0 11: (0: 2 == 2): OK 11: (1: 5 == 5): OK 11: (2: 8 == 8): OK 11: (3: 11 == 11): OK 11: (4: 14 == 14): OK 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 1 11: again: my rank = 2 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 1: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 2: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 1: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 2: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 2 11: again: my rank = 1 11: again: my rank = 0 11: 11: Starting tMPI_Scan test 11: Results from mpi_scan process 0: 11: OK 11: again: my rank = 0 11: again: my rank = 2 11: again: my rank = 1 11: 11: Starting tMPI_Once test 11: Printing this number once: 0 (my rank=2) 11: Printing this number once: 1 (my rank=1) 11: Printing this number once: 3 (my rank=1) 11: Printing this number once: 4 (my rank=1) 11: Printing this number once: 5 (my rank=1) 11: Printing this number once: 6 (my rank=1) 11: Printing this number once: 7 (my rank=1) 11: Printing this number once: 8 (my rank=1) 11: Printing this number once: 9 (my rank=1) 11: I was first for 0, my rank=2 11: Printing this number once: 2 (my rank=0) 11: Done. 11: 11: Finishing.. 11/104 Test #11: threadMPI-mpithreads ...................... Passed 10.25 sec test 12 Start 12: threadMPI-sync_cyclecount 12: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/sync_cyclecount "2" "0" "1" 12: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test 12: Test timeout computed to be: 1500 12: 12: sync_cyclecount. 12: 12: Number of threads: 3 12: 12: Number of counters: 3 12: 12: No cycle count. 12/104 Test #12: threadMPI-sync_cyclecount ................. Passed 0.00 sec test 13 Start 13: threadMPI-mpi_speedtest 13: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mpi_speedtest "-nt" "3" 13: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test 13: Test timeout computed to be: 1500 13: No cycle count. 13: No cycle count. 13: No cycle count. 13/104 Test #13: threadMPI-mpi_speedtest ................... Passed 0.00 sec test 14 Start 14: threadMPI-notmpi 14: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/notmpi "-nt" "3" 14: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test 14: Test timeout computed to be: 1500 14: 14: notmpi. 14: 14: Number of threads: 3 14: 14: This platform supports setting thread affinity 14: My ID=0, i=1000, tid=0xaaaadddef5f0 14: My ID=1, i=1000, tid=0xffff90000be0 14: My ID=2, i=1000, tid=0xffff88000be0 14: Total count: 3000 14/104 Test #14: threadMPI-notmpi .......................... Passed 0.00 sec test 15 Start 15: threadMPI-alloc_check 15: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/alloc_check "-nt" "3" 15: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/external/thread_mpi/test 15: Test timeout computed to be: 1500 15: 15: Memory (de)allocation tester. 15: 15: Number of threads: 3 15: 15: thread 0: got arg 10; total number of hw threads: 12 15: thread 2: got arg 10; total number of hw threads: 12 15: thread 1: got arg 10; total number of hw threads: 12 15: my rank = 0 15: my rank = 1 15: my rank = 2 15: 15: Starting MPI_Sendrecv tests 15: Received: 'Sendrecv hello, from thread 1' 15: Received: 'Sendrecv hello, from thread 2' 15: Received: 'Sendrecv hello, from thread 0' 15: 15: Starting MPI_Bcast test 15: Received: 'Broadcast message 0 from 0' 15: Received: 'Broadcast message 0 from 1' 15: Received: 'Broadcast message 0 from 2' 15: Received: 'Broadcast message 1 from 0' 15: Received: 'Broadcast message 1 from 1' 15: Received: 'Broadcast message 1 from 2' 15: 15: Starting MPI_Gather test 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Finishing.. 15/104 Test #15: threadMPI-alloc_check ..................... Passed 0.00 sec test 16 Start 16: TestUtilsUnitTests 16: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests 16: Test timeout computed to be: 60 16: [==========] Running 81 tests from 8 test suites. 16: [----------] Global test environment set-up. 16: [----------] 10 tests from InteractiveTestHelperTest 16: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 16: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (30 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 16: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 16: [----------] 10 tests from InteractiveTestHelperTest (31 ms total) 16: 16: [----------] 10 tests from NameOfTestFromTupleTest 16: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 16: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 16: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 16: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 16: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 16: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 16: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 16: 16: [----------] 3 tests from RefDataFilenameMakerTest 16: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 16: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 16: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 16: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 16: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 16: 16: [----------] 6 tests from PosixMemstreamTest 16: [ RUN ] PosixMemstreamTest.ConstructsAndDestructs 16: [ OK ] PosixMemstreamTest.ConstructsAndDestructs (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilClosed 16: [ OK ] PosixMemstreamTest.HasAStreamUntilClosed (0 ms) 16: [ RUN ] PosixMemstreamTest.CanFetchString 16: [ OK ] PosixMemstreamTest.CanFetchString (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilStringIsFetched 16: [ OK ] PosixMemstreamTest.HasAStreamUntilStringIsFetched (0 ms) 16: [ RUN ] PosixMemstreamTest.CanWriteToStream 16: [ OK ] PosixMemstreamTest.CanWriteToStream (0 ms) 16: [ RUN ] PosixMemstreamTest.CanCheckBufferWithContents 16: [ OK ] PosixMemstreamTest.CanCheckBufferWithContents (0 ms) 16: [----------] 6 tests from PosixMemstreamTest (0 ms total) 16: 16: [----------] 37 tests from ReferenceDataTest 16: [ RUN ] ReferenceDataTest.HandlesSimpleData 16: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 16: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 16: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringBlockData 16: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesVectorData 16: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceData 16: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectData 16: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 16: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingData 16: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedData 16: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnys 16: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 16: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 16: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 16: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 16: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 16: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 16: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 16: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 16: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesReadingValues 16: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (44 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 16: [----------] 37 tests from ReferenceDataTest (50 ms total) 16: 16: [----------] 7 tests from FloatingPointDifferenceTest 16: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 16: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 16: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 16: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 16: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 16: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 16: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 16: 16: [----------] 4 tests from FloatingPointToleranceTest 16: [ RUN ] FloatingPointToleranceTest.UlpTolerance 16: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 16: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 16: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 16: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 16: 16: [----------] 4 tests from XvgTests 16: [ RUN ] XvgTests.CreateFile 16: [ OK ] XvgTests.CreateFile (0 ms) 16: [ RUN ] XvgTests.CheckMissing 16: [ OK ] XvgTests.CheckMissing (0 ms) 16: [ RUN ] XvgTests.CheckExtra 16: [ OK ] XvgTests.CheckExtra (0 ms) 16: [ RUN ] XvgTests.ReadIncorrect 16: [ OK ] XvgTests.ReadIncorrect (0 ms) 16: [----------] 4 tests from XvgTests (1 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 81 tests from 8 test suites ran. (84 ms total) 16: [ PASSED ] 81 tests. 16/104 Test #16: TestUtilsUnitTests ........................ Passed 0.10 sec test 17 Start 17: TestUtilsMpiUnitTests 17: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/testutils/tests 17: Test timeout computed to be: 60 17: [==========] Running 3 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 1 test from MpiSelfTest 17: [ RUN ] MpiSelfTest.Runs 17: [ OK ] MpiSelfTest.Runs (1 ms) 17: [----------] 1 test from MpiSelfTest (2 ms total) 17: 17: [----------] 2 tests from MpiRefDataTest 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank (2 ms) 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName (1 ms) 17: [----------] 2 tests from MpiRefDataTest (4 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 3 tests from 2 test suites ran. (7 ms total) 17: [ PASSED ] 3 tests. 17/104 Test #17: TestUtilsMpiUnitTests ..................... Passed 0.03 sec test 18 Start 18: UtilityUnitTests 18: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/UtilityUnitTests.xml" 18: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests 18: Test timeout computed to be: 60 18: [==========] Running 495 tests from 68 test suites. 18: [----------] Global test environment set-up. 18: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/0.Comparison 18: [ OK ] AllocatorTest/0.Comparison (0 ms) 18: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.Move 18: [ OK ] AllocatorTest/0.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/0 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/1.Comparison 18: [ OK ] AllocatorTest/1.Comparison (0 ms) 18: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.Move 18: [ OK ] AllocatorTest/1.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/1 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/2.Comparison 18: [ OK ] AllocatorTest/2.Comparison (0 ms) 18: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.Move 18: [ OK ] AllocatorTest/2.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/2 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/3.Comparison 18: [ OK ] AllocatorTest/3.Comparison (0 ms) 18: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.Move 18: [ OK ] AllocatorTest/3.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/3 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/4.Comparison 18: [ OK ] AllocatorTest/4.Comparison (0 ms) 18: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.Move 18: [ OK ] AllocatorTest/4.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/4 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator,gmx::PageAlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/5.Comparison 18: [ OK ] AllocatorTest/5.Comparison (0 ms) 18: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.Move 18: [ OK ] AllocatorTest/5.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/5 (0 ms total) 18: 18: [----------] 1 test from AllocatorUntypedTest 18: [ RUN ] AllocatorUntypedTest.Comparison 18: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 18: [----------] 1 test from AllocatorUntypedTest (0 ms total) 18: 18: [----------] 4 tests from EmptyArrayRefTest 18: [ RUN ] EmptyArrayRefTest.IsEmpty 18: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 18: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 18: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 18: 18: [----------] 1 test from EmptyConstArrayRefTest 18: [ RUN ] EmptyConstArrayRefTest.IsEmpty 18: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 18: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 18: 18: [----------] 8 tests from BoolType 18: [ RUN ] BoolType.ImplicitConversion 18: [ OK ] BoolType.ImplicitConversion (0 ms) 18: [ RUN ] BoolType.FalseByDefault 18: [ OK ] BoolType.FalseByDefault (0 ms) 18: [ RUN ] BoolType.Assignment 18: [ OK ] BoolType.Assignment (0 ms) 18: [ RUN ] BoolType.Copy 18: [ OK ] BoolType.Copy (0 ms) 18: [ RUN ] BoolType.ArrayRefCanBeCreated 18: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 18: [ RUN ] BoolType.CanBeCastToBool 18: [ OK ] BoolType.CanBeCastToBool (0 ms) 18: [ RUN ] BoolType.HasSizeOfBool 18: [ OK ] BoolType.HasSizeOfBool (0 ms) 18: [ RUN ] BoolType.HasAlignmentOfBool 18: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 18: [----------] 8 tests from BoolType (0 ms total) 18: 18: [----------] 4 tests from ArrayRefFromBoolTypeVector 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.Works 18: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 18: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 18: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 18: 18: [----------] 7 tests from CStringUtilityTest 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 18: [ RUN ] CStringUtilityTest.strip_comment 18: [ OK ] CStringUtilityTest.strip_comment (0 ms) 18: [ RUN ] CStringUtilityTest.upstring 18: [ OK ] CStringUtilityTest.upstring (0 ms) 18: [ RUN ] CStringUtilityTest.ltrim 18: [ OK ] CStringUtilityTest.ltrim (0 ms) 18: [ RUN ] CStringUtilityTest.rtrim 18: [ OK ] CStringUtilityTest.rtrim (0 ms) 18: [ RUN ] CStringUtilityTest.trim 18: [ OK ] CStringUtilityTest.trim (0 ms) 18: [----------] 7 tests from CStringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from DefaultInitializationAllocator 18: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 18: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 18: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 18: 18: [----------] 4 tests from EnumerationHelpersTest 18: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 18: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 18: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 18: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 18: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 18: 18: [----------] 1 test from EnumClassSuitsEnumerationArray 18: [ RUN ] EnumClassSuitsEnumerationArray.Works 18: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 18: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 18: 18: [----------] 18 tests from FixedCapacityVectorTest 18: [ RUN ] FixedCapacityVectorTest.IsEmpty 18: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 18: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PushWorks 18: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PopWorks 18: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ResizeWorks 18: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ClearWorks 18: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 18: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.AtThrows 18: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 18: [ RUN ] FixedCapacityVectorTest.IteratorWorks 18: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 18: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 18: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 18: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 18: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.DataWorks 18: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 18: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 18: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 18: 18: [----------] 7 tests from TreeValueTransformTest 18: [ RUN ] TreeValueTransformTest.SimpleTransforms 18: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 18: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 18: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromString 18: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 18: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 18: [ RUN ] TreeValueTransformTest.ScopedTransformRules 18: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 18: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 18: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 18: [----------] 7 tests from TreeValueTransformTest (2 ms total) 18: 18: [----------] 1 test from TreeValueTransformErrorTest 18: [ RUN ] TreeValueTransformErrorTest.ConversionError 18: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms) 18: [----------] 1 test from TreeValueTransformErrorTest (1 ms total) 18: 18: [----------] 9 tests from ListOfLists 18: [ RUN ] ListOfLists.EmptyListOfListsWorks 18: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 18: [ RUN ] ListOfLists.AppendWorks 18: [ OK ] ListOfLists.AppendWorks (0 ms) 18: [ RUN ] ListOfLists.EmptyListWorks 18: [ OK ] ListOfLists.EmptyListWorks (0 ms) 18: [ RUN ] ListOfLists.AppendAccessWorks 18: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 18: [ RUN ] ListOfLists.ClearWorks 18: [ OK ] ListOfLists.ClearWorks (0 ms) 18: [ RUN ] ListOfLists.OutOfRangeAccessThrows 18: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 18: [ RUN ] ListOfLists.FrontAndBackWork 18: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 18: [ RUN ] ListOfLists.ExtractsAndRestores 18: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 18: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 18: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 18: [----------] 9 tests from ListOfLists (0 ms total) 18: 18: [----------] 7 tests from LoggerTest 18: [ RUN ] LoggerTest.EmptyLoggerWorks 18: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToStream 18: [ OK ] LoggerTest.LogsToStream (0 ms) 18: [ RUN ] LoggerTest.LogsToFile 18: [ OK ] LoggerTest.LogsToFile (0 ms) 18: [ RUN ] LoggerTest.LevelFilteringWorks 18: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleStreams 18: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleFiles 18: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 18: [ RUN ] LoggerTest.LogsToStreamAndFile 18: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 18: [----------] 7 tests from LoggerTest (2 ms total) 18: 18: [----------] 7 tests from MessageStringCollectorTest 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 18: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 18: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveAssign 18: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 18: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 18: 18: [----------] 12 tests from MpiComm 18: [ RUN ] MpiComm.SingleRankNoComm 18: [ OK ] MpiComm.SingleRankNoComm (0 ms) 18: [ RUN ] MpiComm.CommWorld 18: [ OK ] MpiComm.CommWorld (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: ./src/gromacs/utility/tests/mpicomm.cpp:160: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:168: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:181: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:194: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 18: [ RUN ] MpiComm.ConstructorThrowsOnNull 18: ./src/gromacs/utility/tests/mpicomm.cpp:206: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull (0 ms) 18: [ RUN ] MpiComm.CopyConstructorWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:220: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CopyConstructorWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:243: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:259: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:281: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:298: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 18: [----------] 12 tests from MpiComm (0 ms total) 18: 18: [----------] 1 test from PathTest 18: [ RUN ] PathTest.StripSourcePrefixWorks 18: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 18: [----------] 1 test from PathTest (0 ms total) 18: 18: [----------] 2 tests from PhysicalNodeCommunicatorTest 18: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 18: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 18: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 18: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 18: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 18: 18: [----------] 5 tests from Range 18: [ RUN ] Range.EmptyRangeWorks 18: [ OK ] Range.EmptyRangeWorks (0 ms) 18: [ RUN ] Range.NonEmptyRangeWorks 18: [ OK ] Range.NonEmptyRangeWorks (0 ms) 18: [ RUN ] Range.BeginEnd 18: [ OK ] Range.BeginEnd (0 ms) 18: [ RUN ] Range.IsInRangeWorks 18: [ OK ] Range.IsInRangeWorks (0 ms) 18: [ RUN ] Range.IteratorWorks 18: [ OK ] Range.IteratorWorks (0 ms) 18: [----------] 5 tests from Range (0 ms total) 18: 18: [----------] 3 tests from ScopeGuardTest 18: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 18: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 18: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 18: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 18: [----------] 3 tests from ScopeGuardTest (0 ms total) 18: 18: [----------] 7 tests from StringConvert 18: [ RUN ] StringConvert.NoResultFromEptyString 18: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 18: [ RUN ] StringConvert.ThreeFloatsSuccessfully 18: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 18: [ RUN ] StringConvert.OneIntSucessfully 18: [ OK ] StringConvert.OneIntSucessfully (0 ms) 18: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 18: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 18: [ RUN ] StringConvert.ThrowsWhenWrongSize 18: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 18: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 18: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 18: [----------] 7 tests from StringConvert (0 ms total) 18: 18: [----------] 7 tests from StringToEnumValueConverterTest 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 18: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 18: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 18: 18: [----------] 9 tests from StringUtilityTest 18: [ RUN ] StringUtilityTest.StartsWith 18: [ OK ] StringUtilityTest.StartsWith (0 ms) 18: [ RUN ] StringUtilityTest.EndsWith 18: [ OK ] StringUtilityTest.EndsWith (0 ms) 18: [ RUN ] StringUtilityTest.StripSuffixIfPresent 18: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 18: [ RUN ] StringUtilityTest.StripString 18: [ OK ] StringUtilityTest.StripString (0 ms) 18: [ RUN ] StringUtilityTest.SplitString 18: [ OK ] StringUtilityTest.SplitString (0 ms) 18: [ RUN ] StringUtilityTest.SplitDelimitedString 18: [ OK ] StringUtilityTest.SplitDelimitedString (20 ms) 18: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 18: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 18: [----------] 9 tests from StringUtilityTest (20 ms total) 18: 18: [----------] 2 tests from FormatStringTest 18: [ RUN ] FormatStringTest.HandlesBasicFormatting 18: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 18: [ RUN ] FormatStringTest.HandlesLongStrings 18: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 18: [----------] 2 tests from FormatStringTest (0 ms total) 18: 18: [----------] 1 test from StringFormatterTest 18: [ RUN ] StringFormatterTest.HandlesBasicFormatting 18: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 18: [----------] 1 test from StringFormatterTest (0 ms total) 18: 18: [----------] 1 test from formatAndJoinTest 18: [ RUN ] formatAndJoinTest.Works 18: [ OK ] formatAndJoinTest.Works (0 ms) 18: [----------] 1 test from formatAndJoinTest (0 ms total) 18: 18: [----------] 1 test from JoinStringsTest 18: [ RUN ] JoinStringsTest.Works 18: [ OK ] JoinStringsTest.Works (0 ms) 18: [----------] 1 test from JoinStringsTest (0 ms total) 18: 18: [----------] 6 tests from ReplaceAllTest 18: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 18: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesNoMatches 18: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 18: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 18: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 18: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 18: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 18: [----------] 6 tests from ReplaceAllTest (0 ms total) 18: 18: [----------] 10 tests from TextLineWrapperTest 18: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 18: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 18: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 18: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectly 18: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndent 18: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 18: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 18: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 18: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 18: [----------] 10 tests from TextLineWrapperTest (5 ms total) 18: 18: [----------] 1 test from PrettyPrintListAsRangeTest 18: [ RUN ] PrettyPrintListAsRangeTest.Works 18: [ OK ] PrettyPrintListAsRangeTest.Works (0 ms) 18: [----------] 1 test from PrettyPrintListAsRangeTest (0 ms total) 18: 18: [----------] 1 test from CompileTimeStringJoin 18: [ RUN ] CompileTimeStringJoin.Works 18: [ OK ] CompileTimeStringJoin.Works (0 ms) 18: [----------] 1 test from CompileTimeStringJoin (0 ms total) 18: 18: [----------] 3 tests from TemplateMPTest 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 18: [----------] 3 tests from TemplateMPTest (0 ms total) 18: 18: [----------] 8 tests from TextWriterTest 18: [ RUN ] TextWriterTest.WritesLines 18: [ OK ] TextWriterTest.WritesLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInParts 18: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 18: [ RUN ] TextWriterTest.WritesWrappedLines 18: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 18: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 18: [ RUN ] TextWriterTest.TracksNewlines 18: [ OK ] TextWriterTest.TracksNewlines (0 ms) 18: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 18: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 18: [ RUN ] TextWriterTest.WritesIndentedLines 18: [ OK ] TextWriterTest.WritesIndentedLines (0 ms) 18: [ RUN ] TextWriterTest.ScopedIndenterWritesIndentedLines 18: [ OK ] TextWriterTest.ScopedIndenterWritesIndentedLines (0 ms) 18: [----------] 8 tests from TextWriterTest (3 ms total) 18: 18: [----------] 4 tests from DumpingTextTest 18: [ RUN ] DumpingTextTest.LegacyIndentingWorks 18: [ OK ] DumpingTextTest.LegacyIndentingWorks (0 ms) 18: [ RUN ] DumpingTextTest.ReportsWhenNotAvailableIdentically 18: [ OK ] DumpingTextTest.ReportsWhenNotAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.QuietWhenAvailableIdentically 18: [ OK ] DumpingTextTest.QuietWhenAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.PrintsTitleAndSizeIdentically 18: [ OK ] DumpingTextTest.PrintsTitleAndSizeIdentically (0 ms) 18: [----------] 4 tests from DumpingTextTest (1 ms total) 18: 18: [----------] 1 test from TypeTraitsTest 18: [ RUN ] TypeTraitsTest.IsIntegralConstant 18: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 18: [----------] 1 test from TypeTraitsTest (0 ms total) 18: 18: [----------] 41 tests from RVecTest 18: [ RUN ] RVecTest.CanBeStoredInVector 18: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAsMutable_rvec 18: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Array 18: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 18: [ RUN ] RVecTest.ComparesEqual 18: [ OK ] RVecTest.ComparesEqual (0 ms) 18: [ RUN ] RVecTest.ComparesUnequal 18: [ OK ] RVecTest.ComparesUnequal (0 ms) 18: [ RUN ] RVecTest.CanAddRVecToRvec 18: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanAddAssignRVecToRvec 18: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractRVecFromRvec 18: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 18: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanDotProductRVecByRvec 18: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanCrossProductRVecByRvec 18: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVecInplace 18: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 18: [ RUN ] RVecTest.CanScaleRVec 18: [ OK ] RVecTest.CanScaleRVec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVec 18: [ OK ] RVecTest.CanDivideRVec (0 ms) 18: [ RUN ] RVecTest.CanDoUnitvFromRVec 18: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanSqLengthOfRVec 18: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanLengthOfRVec 18: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToRVec 18: [ OK ] RVecTest.CanCastToRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToDVec 18: [ OK ] RVecTest.CanCastToDVec (0 ms) 18: [ RUN ] RVecTest.CanLeftScalarMultiply 18: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanRightScalarMultiply 18: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanGetUnitvFromRVec 18: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanGetSqLengthOfRVec 18: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanGetLengthOfRVec 18: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoCrossProductOfRVec 18: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoDotProductOfRVec 18: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanScaleByVector 18: [ OK ] RVecTest.CanScaleByVector (0 ms) 18: [ RUN ] RVecTest.CanNegate 18: [ OK ] RVecTest.CanNegate (0 ms) 18: [ RUN ] RVecTest.asIVec 18: [ OK ] RVecTest.asIVec (0 ms) 18: [ RUN ] RVecTest.elementWiseMin 18: [ OK ] RVecTest.elementWiseMin (0 ms) 18: [ RUN ] RVecTest.elementWiseMax 18: [ OK ] RVecTest.elementWiseMax (0 ms) 18: [ RUN ] RVecTest.WorksAs_dvec_Reference 18: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_ivec_Reference 18: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Reference 18: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 18: [ RUN ] RVecTest.CopyConstructorWorks 18: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 18: [ RUN ] RVecTest.CopyAssignmentWorks 18: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.MoveConstructorWorks 18: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 18: [ RUN ] RVecTest.MoveAssignmentWorks 18: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.UsableInConstexpr 18: [ OK ] RVecTest.UsableInConstexpr (0 ms) 18: [----------] 41 tests from RVecTest (0 ms total) 18: 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 18: 18: [----------] 11 tests from WithInputPaths/PathSearchTest 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (1 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (1 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 18: [----------] 11 tests from WithInputPaths/PathSearchTest (9 ms total) 18: 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 18: 18: [----------] 24 tests from Works/DumpingVectorsTest 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 (0 ms) 18: [----------] 24 tests from Works/DumpingVectorsTest (9 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 495 tests from 68 test suites ran. (60 ms total) 18: [ PASSED ] 485 tests. 18: [ SKIPPED ] 10 tests, listed below: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull 18: [ SKIPPED ] MpiComm.CopyConstructorWorks 18: [ SKIPPED ] MpiComm.AssigmentWorks 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf 18: 18: YOU HAVE 1 DISABLED TEST 18: 18/104 Test #18: UtilityUnitTests .......................... Passed 0.10 sec test 19 Start 19: MpiCommTests 19: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mpicomm-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MpiCommTests.xml" 19: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests 19: Test timeout computed to be: 60 19: [==========] Running 12 tests from 1 test suite. 19: [----------] Global test environment set-up. 19: [----------] 12 tests from MpiComm 19: [ RUN ] MpiComm.SingleRankNoComm 19: [ OK ] MpiComm.SingleRankNoComm (0 ms) 19: [ RUN ] MpiComm.CommWorld 19: [ OK ] MpiComm.CommWorld (36 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (24 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (31 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (13 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (66 ms) 19: [ RUN ] MpiComm.ConstructorThrowsOnNull 19: [ OK ] MpiComm.ConstructorThrowsOnNull (0 ms) 19: [ RUN ] MpiComm.CopyConstructorWorks 19: [ OK ] MpiComm.CopyConstructorWorks (3 ms) 19: [ RUN ] MpiComm.AssigmentWorks 19: [ OK ] MpiComm.AssigmentWorks (3 ms) 19: [ RUN ] MpiComm.AssigmentWorksForSelf 19: [ OK ] MpiComm.AssigmentWorksForSelf (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorks 19: [ OK ] MpiComm.MoveAssigmentWorks (15 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 19: [ OK ] MpiComm.MoveAssigmentWorksForSelf (8 ms) 19: [----------] 12 tests from MpiComm (205 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 12 tests from 1 test suite ran. (205 ms total) 19: [ PASSED ] 12 tests. 19/104 Test #19: MpiCommTests .............................. Passed 0.22 sec test 20 Start 20: UtilityMpiUnitTests 20: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/utility/tests 20: Test timeout computed to be: 60 20: [==========] Running 7 tests from 2 test suites. 20: [----------] Global test environment set-up. 20: [----------] 5 tests from CoordinateExceptionHandlingTest 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow (1 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue (35 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow (33 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow (0 ms) 20: [----------] 5 tests from CoordinateExceptionHandlingTest (71 ms total) 20: 20: [----------] 2 tests from PhysicalNodeCommunicatorTest 20: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 20: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 20: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 20: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 20: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 7 tests from 2 test suites ran. (72 ms total) 20: [ PASSED ] 7 tests. 20/104 Test #20: UtilityMpiUnitTests ....................... Passed 0.09 sec test 21 Start 21: MdlibUnitTest 21: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdlibUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests 21: Test timeout computed to be: 60 21: [==========] Running 1042 tests from 29 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from EffectiveAtomDensity 21: [ RUN ] EffectiveAtomDensity.VolumeIndependence 21: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 21: [ RUN ] EffectiveAtomDensity.WeightingWorks 21: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 21: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 21: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 21: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 21: 21: [----------] 2 tests from AtomNonbondedAndKineticProperties 21: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 21: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 21: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 21: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 21: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 21: 21: [----------] 1 test from VerletBufferConstraintTest 21: [ RUN ] VerletBufferConstraintTest.EqualMasses 21: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 21: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 21: 21: [----------] 1 test from VerletBufferSize 21: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 21: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 21: [----------] 1 test from VerletBufferSize (0 ms total) 21: 21: [----------] 6 tests from CalcvirTest 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 21: [----------] 6 tests from CalcvirTest (2 ms total) 21: 21: [----------] 2 tests from PrEbinTest 21: [ RUN ] PrEbinTest.HandlesAverages 21: [ OK ] PrEbinTest.HandlesAverages (0 ms) 21: [ RUN ] PrEbinTest.HandlesEmptyAverages 21: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 21: [----------] 2 tests from PrEbinTest (1 ms total) 21: 21: [----------] 3 tests from EnergyDriftTracker 21: [ RUN ] EnergyDriftTracker.emptyWorks 21: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.onePointWorks 21: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.manyPointsWorks 21: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 21: [----------] 3 tests from EnergyDriftTracker (0 ms total) 21: 21: [----------] 4 tests from ShakeTest 21: [ RUN ] ShakeTest.ConstrainsOneBond 21: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 21: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 21: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 21: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 21: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 21: [----------] 4 tests from ShakeTest (0 ms total) 21: 21: [----------] 1 test from NullSignalTest 21: [ RUN ] NullSignalTest.NullSignallerWorks 21: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 21: [----------] 1 test from NullSignalTest (0 ms total) 21: 21: [----------] 7 tests from SignalTest 21: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 21: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 21: [----------] 7 tests from SignalTest (0 ms total) 21: 21: [----------] 13 tests from UpdateGroupsTest 21: [ RUN ] UpdateGroupsTest.WithEthaneUA 21: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 21: [ RUN ] UpdateGroupsTest.WithMethane 21: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithEthane 21: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 21: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 21: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFourSite 21: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 21: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 21: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 21: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 21: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 21: [----------] 13 tests from UpdateGroupsTest (0 ms total) 21: 21: [----------] 1 test from UpdateGroupsCog 21: [ RUN ] UpdateGroupsCog.ComputesCogs 21: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 21: [----------] 1 test from UpdateGroupsCog (1 ms total) 21: 21: [----------] 3 tests from VSiteTest 21: [ RUN ] VSiteTest.VSiteLowerConstructingWorks 21: [ OK ] VSiteTest.VSiteLowerConstructingWorks (0 ms) 21: [ RUN ] VSiteTest.VSiteHigherConstructingThrows 21: [ OK ] VSiteTest.VSiteHigherConstructingThrows (3 ms) 21: [ RUN ] VSiteTest.VSiteEqualConstructingThrows 21: [ OK ] VSiteTest.VSiteEqualConstructingThrows (0 ms) 21: [----------] 3 tests from VSiteTest (4 ms total) 21: 21: [----------] 2 tests from WholeMoleculeTransform 21: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 21: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 21: [ RUN ] WholeMoleculeTransform.HandlesReordering 21: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 21: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 21: 21: [----------] 28 tests from WithParameters/ConstraintsTest 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (5 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (6 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 21: [----------] 28 tests from WithParameters/ConstraintsTest (21 ms total) 21: 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 (1 ms) 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest (1 ms total) 21: 21: [----------] 11 tests from WithParameters/EnergyOutputTest 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 21: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 21: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (4 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (1 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (2 ms) 21: [----------] 11 tests from WithParameters/EnergyOutputTest (28 ms total) 21: 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 21: 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 21: 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 21: 21: [----------] 17 tests from WithParameters/LangevinTest 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (1 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 21: [----------] 17 tests from WithParameters/LangevinTest (9 ms total) 21: 21: [----------] 16 tests from WithParameters/LeapFrogTest 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (3 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 21: [----------] 16 tests from WithParameters/LeapFrogTest (23 ms total) 21: 21: [----------] 140 tests from Cubic/ParrRahmTest 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Cubic/ParrRahmTest (51 ms total) 21: 21: [----------] 140 tests from Rectilinear/ParrRahmTest 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (1 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Rectilinear/ParrRahmTest (51 ms total) 21: 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (50 ms total) 21: 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (52 ms total) 21: 21: [----------] 140 tests from TruncOct/ParrRahmTest 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from TruncOct/ParrRahmTest (52 ms total) 21: 21: [----------] 140 tests from Other/ParrRahmTest 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Other/ParrRahmTest (56 ms total) 21: 21: [----------] 13 tests from WithParameters/SettleTest 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 21: [----------] 13 tests from WithParameters/SettleTest (15 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1042 tests from 29 test suites ran. (427 ms total) 21: [ PASSED ] 1042 tests. 21/104 Test #21: MdlibUnitTest ............................. Passed 6.61 sec test 22 Start 22: AwhTest 22: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/AwhTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/awh/tests 22: Test timeout computed to be: 60 22: [==========] Running 27 tests from 10 test suites. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from SerializationTest 22: [ RUN ] SerializationTest.CanSerializeDimParams 22: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeBiasParams 22: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeAwhParams 22: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 22: [----------] 3 tests from SerializationTest (0 ms total) 22: 22: [----------] 1 test from BiasTest 22: [ RUN ] BiasTest.DetectsCovering 22: [ OK ] BiasTest.DetectsCovering (0 ms) 22: [----------] 1 test from BiasTest (0 ms total) 22: 22: [----------] 1 test from biasGridTest 22: [ RUN ] biasGridTest.neighborhood 22: [ OK ] biasGridTest.neighborhood (1 ms) 22: [----------] 1 test from biasGridTest (1 ms total) 22: 22: [----------] 2 tests from BiasSharingTest 22: [ RUN ] BiasSharingTest.SharingWorks 22: [ OK ] BiasSharingTest.SharingWorks (59 ms) 22: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 22: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (114 ms) 22: [----------] 2 tests from BiasSharingTest (173 ms total) 22: 22: [----------] 2 tests from BiasFepLambdaStateTest 22: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 22: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 22: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 22: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 22: [----------] 2 tests from BiasFepLambdaStateTest (1 ms total) 22: 22: [----------] 8 tests from WithParameters/BiasTest 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 22: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 22: 22: [----------] 2 tests from WithParameters/BiasStateTest 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 22: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 22: 22: [----------] 1 test from WithParameters/UserInputTest 22: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 22: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 22: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 22: 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (4 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (4 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (4 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (4 ms) 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (18 ms total) 22: 22: [----------] 3 tests from WithParameters/FrictionMetricTest 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (12 ms) 22: [----------] 3 tests from WithParameters/FrictionMetricTest (15 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 27 tests from 10 test suites ran. (219 ms total) 22: [ PASSED ] 27 tests. 22/104 Test #22: AwhTest ................................... Passed 0.24 sec test 23 Start 23: DensityFittingAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/densityfitting/tests 23: Test timeout computed to be: 60 23: [==========] Running 18 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from DensityFittingTest 23: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 23: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 23: [ RUN ] DensityFittingTest.SingleAtom 23: [ OK ] DensityFittingTest.SingleAtom (0 ms) 23: [----------] 2 tests from DensityFittingTest (1 ms total) 23: 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest 23: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 23: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 23: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 23: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 23: 23: [----------] 1 test from DensityFittingForceProviderState 23: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 23: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 23: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 23: 23: [----------] 8 tests from DensityFittingOptionsTest 23: [ RUN ] DensityFittingOptionsTest.DefaultParameters 23: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 23: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 23: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 23: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 23: [ RUN ] DensityFittingOptionsTest.KvtToInternal 23: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 23: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 23: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 23: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 18 tests from 4 test suites ran. (3 ms total) 23: [ PASSED ] 18 tests. 23/104 Test #23: DensityFittingAppliedForcesUnitTest ....... Passed 0.02 sec test 24 Start 24: QMMMAppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests 24: Test timeout computed to be: 60 24: [==========] Running 28 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 2 tests from QMMMInputGeneratorTest 24: [ RUN ] QMMMInputGeneratorTest.CanConstruct 24: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 24: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 24: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 24: [----------] 2 tests from QMMMInputGeneratorTest (0 ms total) 24: 24: [----------] 6 tests from QMMMTopologyPreprocessorTest 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Setting the LD random seed to -2195668 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (5 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Setting the LD random seed to -1418334498 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (3 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading -0.41000 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -310051201 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (4 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 63.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 129.093 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -1610651858 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (12 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: 24: NOTE 2 [file unknown]: 24: You are using constraints on all bonds, whereas the forcefield has been 24: parametrized only with constraints involving hydrogen atoms. We suggest 24: using constraints = h-bonds instead, this will also improve performance. 24: 24: 24: NOTE 3 [file unknown]: 24: For energy conservation with LINCS, lincs_iter should be 2 or larger. 24: 24: 24: Number of degrees of freedom in T-Coupling group rest is 42.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 193.640 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 5 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: 24: WARNING 2 [file unknown]: 24: Your embedded subsystem has a lot of constrained bonds. They probably 24: have been generated automatically. That could produce artifacts in the 24: simulation. Consider constraints = none in the mdp file. 24: 24: 24: Setting the LD random seed to -39920737 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: turning all bonds into constraints... 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (10 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Number of degrees of freedom in T-Coupling group rest is 45.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.3-Debian_1 (single precision) 24: Setting the LD random seed to -281678098 24: 24: Generated 3 of the 6 non-bonded parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'VSTEST' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 24: 24: Cleaning up constraints and constant bonded interactions with virtual sites 24: Analysing residue names: 24: There are: 1 Other residues 24: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (5 ms) 24: [----------] 6 tests from QMMMTopologyPreprocessorTest (42 ms total) 24: 24: [----------] 9 tests from QMMMOptionsTest 24: [ RUN ] QMMMOptionsTest.DefaultParameters 24: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 24: [ RUN ] QMMMOptionsTest.OptionSetsActive 24: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 24: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 24: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 24: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 24: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 24: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 24: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 24: [----------] 9 tests from QMMMOptionsTest (3 ms total) 24: 24: [----------] 3 tests from QMMMForceProviderStateTest 24: [ RUN ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint 24: [ OK ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent 24: [ OK ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.MissingStateWhenNoData 24: [ OK ] QMMMForceProviderStateTest.MissingStateWhenNoData (0 ms) 24: [----------] 3 tests from QMMMForceProviderStateTest (0 ms total) 24: 24: [----------] 1 test from QMMMForceProviderTest 24: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 24: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 24: [----------] 1 test from QMMMForceProviderTest (0 ms total) 24: 24: [----------] 1 test from QMMMTest 24: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 24: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 24: [----------] 1 test from QMMMTest (0 ms total) 24: 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink (0 ms) 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest (3 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 28 tests from 7 test suites ran. (51 ms total) 24: [ PASSED ] 28 tests. 24/104 Test #24: QMMMAppliedForcesUnitTest ................. Passed 0.07 sec test 25 Start 25: ColvarsAppliedForcesUnitTest 25: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests 25: Test timeout computed to be: 60 25: [==========] Running 16 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 1 test from ColvarsTest 25: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 25: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 25: [----------] 1 test from ColvarsTest (0 ms total) 25: 25: [----------] 6 tests from ColvarsOptionsTest 25: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 25: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OptionSetsActive 25: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to -8667201 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (14 ms) 25: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 25: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 25: [----------] 6 tests from ColvarsOptionsTest (16 ms total) 25: 25: [----------] 4 tests from ColvarsPreProcessorTest 25: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to -402917065 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (4 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to -403715009 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (5 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to 1453276653 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (4 ms) 25: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to -10553425 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (7 ms) 25: [----------] 4 tests from ColvarsPreProcessorTest (22 ms total) 25: 25: [----------] 5 tests from ColvarsForceProviderTest 25: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 25: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 25: [ RUN ] ColvarsForceProviderTest.SimpleInputs 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to -471867910 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.SimpleInputs (4 ms) 25: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to -2059479425 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (4 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to 267242295 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForces4water (15 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 66.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: NVE simulation: will use the initial temperature of 300.368 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.3-Debian_1 (single precision) 25: Setting the LD random seed to -807472387 25: 25: Generated 2211 of the 2211 non-bonded parameter combinations 25: 25: Generated 2211 of the 2211 1-4 parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 25: Analysing residue names: 25: There are: 2 Protein residues 25: Analysing Protein... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (21 ms) 25: [----------] 5 tests from ColvarsForceProviderTest (47 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 16 tests from 4 test suites ran. (86 ms total) 25: [ PASSED ] 16 tests. 25/104 Test #25: ColvarsAppliedForcesUnitTest .............. Passed 0.10 sec test 26 Start 26: PlumedAppliedForcesUnitTests 26: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests 26: Test timeout computed to be: 60 26: [==========] Running 8 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 8 tests from PlumedOptionsTest 26: [ RUN ] PlumedOptionsTest.defaultConstructor 26: [ OK ] PlumedOptionsTest.defaultConstructor (1 ms) 26: [ RUN ] PlumedOptionsTest.setTimeStep 26: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 26: [ RUN ] PlumedOptionsTest.setStartingBehavior 26: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFile 26: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 26: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 26: [ RUN ] PlumedOptionsTest.setTopology 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 21.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: 26: NOTE 2 [file angles1.top, line 72]: 26: In moleculetype 'butane' 4 atoms are not bound by a potential or 26: constraint to any other atom in the same moleculetype. Although 26: technically this might not cause issues in a simulation, this often means 26: that the user forgot to add a bond/potential/constraint or put multiple 26: molecules in the same moleculetype definition by mistake. Run with -v to 26: get information for each atom. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: NVE simulation: will use the initial temperature of 238.919 K for 26: determining the Verlet buffer size 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.3-Debian_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.3-Debian_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 17493.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: NVE simulation: will use the initial temperature of 67.983 K for 26: determining the Verlet buffer size 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.3-Debian_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.3-Debian_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.3-Debian_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.3-Debian_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.3-Debian_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.3-Debian_1 (single precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 18.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: NVE simulation: will use the initial temperature of 135.187 K for 26: determining the Verlet buffer size 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.3-Debian_1 (single precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.3-Debian_1 (single precision) 26: Setting the LD random seed to -312480773 26: 26: Generated 10 of the 10 non-bonded parameter combinations 26: 26: Generated 10 of the 10 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Water residues 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -134219277 26: 26: Generated 3 of the 3 non-bonded parameter combinations 26: 26: Excluding 3 bonded neighbours molecule type 'butane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/angles1.gro' 26: Analysing residue names: 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -25174051 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Argon' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon5832.gro' 26: Analysing residue names: 26: There are: 5832 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -16793108 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonA' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonB' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonC' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonD' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -422093489 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Dipole' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 26: Analysing residue names: 26: There are: 2 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -537993223 26: 26: Generated 331705 of the 331705 non-bonded parameter combinations 26: 26: Generated 331705 of the 331705 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Excluding 3 bonded neighbours molecule type 'methane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 26: Analysing residue names: 26: There are: 1 Water residues 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: [ OK ] PlumedOptionsTest.setTopology (236 ms) 26: [----------] 8 tests from PlumedOptionsTest (243 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 8 tests from 1 test suite ran. (243 ms total) 26: [ PASSED ] 8 tests. 26/104 Test #26: PlumedAppliedForcesUnitTests .............. Passed 0.27 sec test 27 Start 27: PlumedMDTests 27: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/PlumedMDTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/plumed/tests 27: Test timeout computed to be: 600 27: [==========] Running 2 tests from 1 test suite. 27: [----------] Global test environment set-up. 27: [----------] 2 tests from SimplePlumedMD/PlumedRun 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 27: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 2 tests from 1 test suite ran. (8 ms total) 27: [ PASSED ] 0 tests. 27: [ SKIPPED ] 2 tests, listed below: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27/104 Test #27: PlumedMDTests ............................. Passed 0.02 sec test 28 Start 28: NNPotAppliedForcesUnitTest 28: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 28: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests 28: Test timeout computed to be: 60 28: [==========] Running 17 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 1 test from NNPotTest 28: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 28: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 28: [----------] 1 test from NNPotTest (0 ms total) 28: 28: [----------] 5 tests from NNPotOptionsTest 28: [ RUN ] NNPotOptionsTest.DefaultParameters 28: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 28: [ RUN ] NNPotOptionsTest.OptionSetsActive 28: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 28: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 28: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 28: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 28: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 28: [----------] 5 tests from NNPotOptionsTest (1 ms total) 28: 28: [----------] 1 test from NNPotForceProviderTest 28: [ RUN ] NNPotForceProviderTest.CanConstruct 28: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 28: [----------] 1 test from NNPotForceProviderTest (0 ms total) 28: 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Setting the LD random seed to 1458171199 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 (4 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Setting the LD random seed to -1250051203 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 (4 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Setting the LD random seed to 1874850551 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 (5 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Setting the LD random seed to 1068497827 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 (4 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Setting the LD random seed to -50877062 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 (9 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: Setting the LD random seed to -1048771 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 (10 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: 28: WARNING 1 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -34835 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 (9 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (single precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: 28: WARNING 2 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -185339905 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 (9 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Setting the LD random seed to -134268991 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 (4 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.3-Debian_1 (single precision) 28: Setting the LD random seed to -270901253 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 (4 ms) 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest (69 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 17 tests from 4 test suites ran. (71 ms total) 28: [ PASSED ] 17 tests. 28/104 Test #28: NNPotAppliedForcesUnitTest ................ Passed 0.10 sec test 29 Start 29: AppliedForcesUnitTest 29: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 29: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/applied_forces/tests 29: Test timeout computed to be: 60 29: [==========] Running 3 tests from 1 test suite. 29: [----------] Global test environment set-up. 29: [----------] 3 tests from ElectricFieldTest 29: [ RUN ] ElectricFieldTest.Static 29: [ OK ] ElectricFieldTest.Static (0 ms) 29: [ RUN ] ElectricFieldTest.Oscillating 29: [ OK ] ElectricFieldTest.Oscillating (0 ms) 29: [ RUN ] ElectricFieldTest.Pulsed 29: [ OK ] ElectricFieldTest.Pulsed (0 ms) 29: [----------] 3 tests from ElectricFieldTest (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 3 tests from 1 test suite ran. (0 ms total) 29: [ PASSED ] 3 tests. 29/104 Test #29: AppliedForcesUnitTest ..................... Passed 0.01 sec test 30 Start 30: ListedForcesTest 30: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/ListedForcesTest.xml" 30: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/listed_forces/tests 30: Test timeout computed to be: 60 30: [==========] Running 132 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from Bond/ListedForcesTest 30: [ RUN ] Bond/ListedForcesTest.Ifunc/0 30: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/1 30: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/2 30: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/3 30: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/4 30: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/5 30: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/6 30: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/7 30: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/8 30: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/9 30: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/10 30: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/11 30: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/12 30: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/13 30: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/14 30: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/15 30: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/16 30: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/17 30: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/18 30: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/19 30: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/20 30: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/21 30: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/22 30: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/23 30: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 30: [----------] 24 tests from Bond/ListedForcesTest (12 ms total) 30: 30: [----------] 33 tests from Angle/ListedForcesTest 30: [ RUN ] Angle/ListedForcesTest.Ifunc/0 30: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/1 30: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/2 30: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/3 30: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/4 30: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/5 30: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/6 30: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/7 30: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/8 30: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/9 30: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/10 30: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/11 30: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/12 30: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/13 30: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/14 30: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/15 30: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/16 30: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/17 30: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/18 30: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/19 30: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/20 30: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/21 30: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/22 30: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/23 30: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/24 30: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/25 30: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/26 30: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/27 30: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/28 30: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/29 30: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/30 30: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/31 30: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/32 30: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 30: [----------] 33 tests from Angle/ListedForcesTest (15 ms total) 30: 30: [----------] 18 tests from Dihedral/ListedForcesTest 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Dihedral/ListedForcesTest (8 ms total) 30: 30: [----------] 12 tests from Polarize/ListedForcesTest 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 30: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 30: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 30: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 30: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 30: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 30: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 30: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 30: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 30: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 30: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 30: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 30: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from Polarize/ListedForcesTest (5 ms total) 30: 30: [----------] 18 tests from Restraints/ListedForcesTest 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 30: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 30: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 30: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 30: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 30: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 30: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 30: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 30: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 30: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 30: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 30: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 30: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 30: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 30: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 30: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 30: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 30: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 30: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Restraints/ListedForcesTest (8 ms total) 30: 30: [----------] 3 tests from BondZeroLength/ListedForcesTest 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total) 30: 30: [----------] 3 tests from AngleZero/ListedForcesTest 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total) 30: 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (6 ms total) 30: 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (1 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (6 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 132 tests from 9 test suites ran. (66 ms total) 30: [ PASSED ] 132 tests. 30/104 Test #30: ListedForcesTest .......................... Passed 0.09 sec test 31 Start 31: NbnxmTests 31: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nbnxm-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbnxmTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests 31: Test timeout computed to be: 60 31: [==========] Running 532 tests from 5 test suites. 31: [----------] Global test environment set-up. 31: [----------] 19 tests from KernelSetupTest 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 31: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 31: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeNone 31: [ OK ] KernelSetupTest.getCoulombKernelTypeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 31: [----------] 19 tests from KernelSetupTest (1 ms total) 31: 31: [----------] 2 tests from SimdEnergyAccumulatorTest 31: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 31: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 31: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 31: 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (1 ms total) 31: 31: [----------] 504 tests from Combinations/NbnxmKernelTest 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [----------] 504 tests from Combinations/NbnxmKernelTest (419 ms total) 31: 31: [----------] 4 tests from WithParameters/PlainPairlistTest 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 (1 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:241: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 (0 ms) 31: [----------] 4 tests from WithParameters/PlainPairlistTest (2 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 532 tests from 5 test suites ran. (425 ms total) 31: [ PASSED ] 189 tests. 31: [ SKIPPED ] 343 tests, listed below: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31/104 Test #31: NbnxmTests ................................ Passed 0.46 sec test 32 Start 32: NbnxmGpuTests 32: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/NbnxmGpuTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests 32: Test timeout computed to be: 60 32: This test program does NOT link in any test case. Please make sure this is intended. 32: [==========] Running 0 tests from 0 test suites. 32: [==========] 0 tests from 0 test suites ran. (0 ms total) 32: [ PASSED ] 0 tests. 32/104 Test #32: NbnxmGpuTests ............................. Passed 0.02 sec test 33 Start 33: GmxlibTests 33: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GmxlibTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests 33: Test timeout computed to be: 60 33: [==========] Running 78 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 72 tests from NBInteraction/NonbondedFepTest 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (2 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 33: [----------] 72 tests from NBInteraction/NonbondedFepTest (45 ms total) 33: 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (3 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 78 tests from 2 test suites ran. (49 ms total) 33: [ PASSED ] 78 tests. 33/104 Test #33: GmxlibTests ............................... Passed 0.08 sec test 34 Start 34: GmxlibGpuTests 34: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/nonbonded-fep-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GmxlibGpuTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/nbnxm/tests 34: Test timeout computed to be: 60 34: This test program does NOT link in any test case. Please make sure this is intended. 34: [==========] Running 0 tests from 0 test suites. 34: [==========] 0 tests from 0 test suites ran. (0 ms total) 34: [ PASSED ] 0 tests. 34/104 Test #34: GmxlibGpuTests ............................ Passed 0.02 sec test 35 Start 35: CommandLineUnitTests 35: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests 35: Test timeout computed to be: 60 35: [==========] Running 60 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from CommandLineHelpModuleTest 35: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 35: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms) 35: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 35: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 35: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 35: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 35: [----------] 3 tests from CommandLineHelpModuleTest (4 ms total) 35: 35: [----------] 7 tests from CommandLineHelpWriterTest 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 35: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 35: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 35: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 35: [----------] 7 tests from CommandLineHelpWriterTest (4 ms total) 35: 35: [----------] 6 tests from CommandLineModuleManagerTest 35: [ RUN ] CommandLineModuleManagerTest.RunsModule 35: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 35: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 35: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 35: 35: [----------] 13 tests from CommandLineParserTest 35: [ RUN ] CommandLineParserTest.HandlesSingleValues 35: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 35: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 35: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesString 35: [ OK ] CommandLineParserTest.HandlesString (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 35: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 35: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 35: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 35: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 35: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 35: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 35: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 35: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 35: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 35: [----------] 13 tests from CommandLineParserTest (0 ms total) 35: 35: [----------] 6 tests from CommandLineProgramContextTest 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 35: [----------] 6 tests from CommandLineProgramContextTest (1 ms total) 35: 35: [----------] 3 tests from OutputNamesTest 35: [ RUN ] OutputNamesTest.CanBeSuffixed 35: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 35: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 35: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 35: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 35: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 35: [----------] 3 tests from OutputNamesTest (0 ms total) 35: 35: [----------] 22 tests from ParseCommonArgsTest 35: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 35: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 35: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 35: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 35: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 35: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 35: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 35: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 35: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 35: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 35: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 35: Value is /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 35: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 35: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 35: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 35: [----------] 22 tests from ParseCommonArgsTest (3 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 60 tests from 7 test suites ran. (16 ms total) 35: [ PASSED ] 60 tests. 35/104 Test #35: CommandLineUnitTests ...................... Passed 0.03 sec test 36 Start 36: DomDecTests 36: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/DomDecTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests 36: Test timeout computed to be: 60 36: [==========] Running 9 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 7 tests from HashedMap 36: [ RUN ] HashedMap.InsertsFinds 36: [ OK ] HashedMap.InsertsFinds (0 ms) 36: [ RUN ] HashedMap.NegativeKeysWork 36: [ OK ] HashedMap.NegativeKeysWork (0 ms) 36: [ RUN ] HashedMap.InsertsErases 36: [ OK ] HashedMap.InsertsErases (0 ms) 36: [ RUN ] HashedMap.InsertsOrAssigns 36: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 36: [ RUN ] HashedMap.Clears 36: [ OK ] HashedMap.Clears (0 ms) 36: [ RUN ] HashedMap.LinkedEntries 36: [ OK ] HashedMap.LinkedEntries (0 ms) 36: [ RUN ] HashedMap.ResizesTable 36: [ OK ] HashedMap.ResizesTable (0 ms) 36: [----------] 7 tests from HashedMap (0 ms total) 36: 36: [----------] 2 tests from LocalAtomSetManager 36: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 36: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 36: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 36: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 36: [----------] 2 tests from LocalAtomSetManager (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 9 tests from 2 test suites ran. (0 ms total) 36: [ PASSED ] 9 tests. 36/104 Test #36: DomDecTests ............................... Passed 0.01 sec test 37 Start 37: DomDecMpiTests 37: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/DomDecMpiTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/domdec/tests 37: Test timeout computed to be: 60 37: [==========] Running 8 tests from 1 test suite. 37: [----------] Global test environment set-up. 37: [----------] 8 tests from Works/HaloExchangeTest 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/0 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/0 (13 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/1 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/1 (11 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/2 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/2 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/3 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/3 (10 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 (0 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/3 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 (0 ms) 37: [----------] 8 tests from Works/HaloExchangeTest (39 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 8 tests from 1 test suite ran. (39 ms total) 37: [ PASSED ] 4 tests. 37: [ SKIPPED ] 4 tests, listed below: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 37/104 Test #37: DomDecMpiTests ............................ Passed 0.06 sec test 38 Start 38: EwaldUnitTests 38: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/EwaldUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/ewald/tests 38: Test timeout computed to be: 60 38: [==========] Running 407 tests from 9 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from SeparatePmeRanksPermittedTest 38: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 38: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 38: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 38: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 38: 38: [----------] 108 tests from Pme_SplineAndSpreadTest 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (6 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (3 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 38: [----------] 108 tests from Pme_SplineAndSpreadTest (173 ms total) 38: 38: [----------] 64 tests from Pme_SolveTest 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from Pme_SolveTest (42 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (14 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (17 ms total) 38: 38: [----------] 64 tests from PmeDiffEps_SolveTest 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from PmeDiffEps_SolveTest (36 ms total) 38: 38: [----------] 72 tests from Pme_GatherTest 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (2 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [----------] 72 tests from Pme_GatherTest (72 ms total) 38: 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (2 ms total) 38: 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (3 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (44 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 407 tests from 9 test suites ran. (404 ms total) 38: [ PASSED ] 311 tests. 38: [ SKIPPED ] 96 tests, listed below: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38/104 Test #38: EwaldUnitTests ............................ Passed 0.44 sec test 39 Start 39: FFTUnitTests 39: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/FFTUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fft/tests 39: Test timeout computed to be: 1920 39: [==========] Running 15 tests from 4 test suites. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from ManyFFTTest 39: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (4 ms) 39: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (8 ms) 39: [----------] 2 tests from ManyFFTTest (13 ms total) 39: 39: [----------] 1 test from FFTTest 39: [ RUN ] FFTTest.Real2DLength18_15Test 39: [ OK ] FFTTest.Real2DLength18_15Test (2 ms) 39: [----------] 1 test from FFTTest (2 ms total) 39: 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (1 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (4 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (7 ms) 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (19 ms total) 39: 39: [----------] 2 tests from Works/ParameterizedFFTTest3D 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 39: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 15 tests from 4 test suites ran. (37 ms total) 39: [ PASSED ] 15 tests. 39/104 Test #39: FFTUnitTests .............................. Passed 0.06 sec test 40 Start 40: FmmInterfaceUnitTests 40: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/fmm-interface-tests "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/FmmInterfaceUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fmm/tests 40: Test timeout computed to be: 60 40: [==========] Running 18 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 10 tests from FmmMdpOptionsTest 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues 40: [ OK ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive 40: [ OK ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive (0 ms) 40: [----------] 10 tests from FmmMdpOptionsTest (1 ms total) 40: 40: [----------] 4 tests from FmmMdpValidatorTest 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings 40: 40: ERROR 1 [file unknown]: 40: ExaFMM expansion order must be greater than 0. 40: 40: 40: ERROR 1 [file unknown]: 40: ExaFMM direct range must be 2 when using GROMACS as a direct provider. 40: 40: 40: ERROR 1 [file unknown]: 40: Adaptive tree cannot be used for FMM when GROMACS is the direct provider. 40: Use a uniform tree instead. 40: 40: 40: ERROR 1 [file unknown]: 40: Maximum particles per cell for FMM must be set to a positive value when 40: using an adaptive tree. 40: 40: 40: ERROR 1 [file unknown]: 40: Tree depth for FMM is determined based on the domain decomposition grid 40: when using GROMACS as the direct provider and should not be set by the 40: user. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings 40: 40: ERROR 1 [file unknown]: 40: FMSolvr tree depth must be greater than or equal to 0. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings 40: [ OK ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm 40: 40: ERROR 1 [file unknown]: 40: FMM requires Coulomb interaction type to be FMM, but got PME 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm (0 ms) 40: [----------] 4 tests from FmmMdpValidatorTest (0 ms total) 40: 40: [----------] 1 test from FmmForceProviderTest 40: [ RUN ] FmmForceProviderTest.ThrowsWhenConstructingStub 40: [ OK ] FmmForceProviderTest.ThrowsWhenConstructingStub (0 ms) 40: [----------] 1 test from FmmForceProviderTest (0 ms total) 40: 40: [----------] 3 tests from FmmForceProviderBuilderTest 40: [ RUN ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady 40: [ OK ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup 40: [ OK ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider 40: [ OK ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider (0 ms) 40: [----------] 3 tests from FmmForceProviderBuilderTest (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 18 tests from 4 test suites ran. (2 ms total) 40: [ PASSED ] 18 tests. 40/104 Test #40: FmmInterfaceUnitTests ..................... Passed 0.02 sec test 41 Start 41: GpuUtilsUnitTests 41: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests 41: Test timeout computed to be: 60 41: [==========] Running 67 tests from 22 test suites. 41: [----------] Global test environment set-up. 41: [----------] 2 tests from ClfftInitializer 41: [ RUN ] ClfftInitializer.SingleInitializationWorks 41: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 41: [ RUN ] ClfftInitializer.TwoInitializationsWork 41: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 41: [----------] 2 tests from ClfftInitializer (0 ms total) 41: 41: [----------] 1 test from DevicesAvailable 41: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 41: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 41: [----------] 1 test from DevicesAvailable (0 ms total) 41: 41: [----------] 1 test from DeviceStreamManagerTest 41: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 41: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 41: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 41: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 41: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 41: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 41: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Swap 41: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Comparison 41: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 41: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 41: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Swap 41: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Comparison 41: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 41: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Swap 41: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Comparison 41: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 41: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Swap 41: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Comparison 41: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 41: 41: [----------] 1 test from HostAllocatorUntypedTest 41: [ RUN ] HostAllocatorUntypedTest.Comparison 41: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 41: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.Move 41: [ OK ] AllocatorTest/0.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/0 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.Move 41: [ OK ] AllocatorTest/1.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/1 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator,gmx::HostAllocationPolicy> 41: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.Move 41: [ OK ] AllocatorTest/2.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/2 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.Move 41: [ OK ] AllocatorTest/3.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/3 (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 67 tests from 22 test suites ran. (0 ms total) 41: [ PASSED ] 67 tests. 41/104 Test #41: GpuUtilsUnitTests ......................... Passed 0.02 sec test 42 Start 42: GpuUtilsMpiTests 42: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/gpu_utils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GpuUtilsMpiTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gpu_utils/tests 42: Test timeout computed to be: 60 42: [==========] Running 15 tests from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message (0 ms) 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/0_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/1_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/12000_values_in_message 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message (0 ms) 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest (2 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 15 tests from 1 test suite ran. (2 ms total) 42: [ PASSED ] 0 tests. 42: [ SKIPPED ] 15 tests, listed below: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: 42: YOU HAVE 3 DISABLED TESTS 42: 42/104 Test #42: GpuUtilsMpiTests .......................... Passed 0.03 sec test 43 Start 43: HardwareUnitTests 43: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/HardwareUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/hardware/tests 43: Test timeout computed to be: 60 43: [==========] Running 22 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 1 test from CpuInfoTest 43: [ RUN ] CpuInfoTest.SupportLevel 43: [ OK ] CpuInfoTest.SupportLevel (0 ms) 43: [----------] 1 test from CpuInfoTest (0 ms total) 43: 43: [----------] 4 tests from HardwareTopologyTest 43: [ RUN ] HardwareTopologyTest.Execute 43: [ OK ] HardwareTopologyTest.Execute (7 ms) 43: [ RUN ] HardwareTopologyTest.HwlocExecute 43: [ OK ] HardwareTopologyTest.HwlocExecute (6 ms) 43: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 43: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (7 ms) 43: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 43: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (7 ms) 43: [----------] 4 tests from HardwareTopologyTest (28 ms total) 43: 43: [----------] 1 test from DevicesManagerTest 43: [ RUN ] DevicesManagerTest.Serialization 43: [ OK ] DevicesManagerTest.Serialization (0 ms) 43: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 43: [----------] 1 test from DevicesManagerTest (0 ms total) 43: 43: [----------] 1 test from UuidStringTest 43: [ RUN ] UuidStringTest.Works 43: [ OK ] UuidStringTest.Works (0 ms) 43: [----------] 1 test from UuidStringTest (0 ms total) 43: 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (3 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (7 ms total) 43: 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (3 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (7 ms total) 43: 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (2 ms) 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (4 ms total) 43: 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (14 ms) 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (14 ms total) 43: 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (18 ms) 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (18 ms total) 43: 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 43: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (26 ms) 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (26 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 22 tests from 10 test suites ran. (107 ms total) 43: [ PASSED ] 22 tests. 43: 43: YOU HAVE 1 DISABLED TEST 43: 43/104 Test #43: HardwareUnitTests ......................... Passed 0.12 sec test 44 Start 44: MathUnitTests 44: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MathUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/math/tests 44: Test timeout computed to be: 60 44: [==========] Running 293 tests from 40 test suites. 44: [----------] Global test environment set-up. 44: [----------] 1 test from EmptyArrayRefWithPaddingTest 44: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 44: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 44: 44: [----------] 2 tests from InvertBoxMatrixTest 44: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 44: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 44: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 44: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 44: 44: [----------] 8 tests from ComplexNumberTest 44: [ RUN ] ComplexNumberTest.RealComplexMultiply 44: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 44: [ RUN ] ComplexNumberTest.RealComplexExp 44: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAdd 44: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexSubtract 44: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexMultiply 44: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexDivision 44: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexConjugate 44: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAbs2 44: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 44: [----------] 8 tests from ComplexNumberTest (2 ms total) 44: 44: [----------] 11 tests from TranslateAndScaleTest 44: [ RUN ] TranslateAndScaleTest.identityTransformation 44: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 44: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 44: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingIdentity 44: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 44: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 44: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 44: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 44: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 44: 44: [----------] 3 tests from AffineTransformationTest 44: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 44: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 44: [ RUN ] AffineTransformationTest.applyTransformationToVectors 44: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 44: [ RUN ] AffineTransformationTest.retrieveGradient 44: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 44: [----------] 3 tests from AffineTransformationTest (0 ms total) 44: 44: [----------] 14 tests from DensitySimilarityTest 44: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 44: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (13 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (13 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationCorrect 44: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 44: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 44: [----------] 14 tests from DensitySimilarityTest (28 ms total) 44: 44: [----------] 6 tests from StructureSimilarityTest 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 44: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 44: [----------] 6 tests from StructureSimilarityTest (0 ms total) 44: 44: [----------] 8 tests from ExponentialMovingAverage 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 44: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 44: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 44: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 44: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 44: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 44: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 44: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 44: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 44: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 44: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 44: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 44: 44: [----------] 21 tests from FunctionTest 44: [ RUN ] FunctionTest.StaticLog2 44: [ OK ] FunctionTest.StaticLog2 (0 ms) 44: [ RUN ] FunctionTest.Log2I32Bit 44: [ OK ] FunctionTest.Log2I32Bit (0 ms) 44: [ RUN ] FunctionTest.Log2I64Bit 44: [ OK ] FunctionTest.Log2I64Bit (0 ms) 44: [ RUN ] FunctionTest.GreatestCommonDivisor 44: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 44: [ RUN ] FunctionTest.InvsqrtFloat 44: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvsqrtDouble 44: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvsqrtInteger 44: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 44: [ RUN ] FunctionTest.InvcbrtFloat 44: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvcbrtDouble 44: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvcbrtInteger 44: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 44: [ RUN ] FunctionTest.SixthrootFloat 44: [ OK ] FunctionTest.SixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.SixthrootDouble 44: [ OK ] FunctionTest.SixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.SixthrootInteger 44: [ OK ] FunctionTest.SixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootFloat 44: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootDouble 44: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootInteger 44: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.Powers 44: [ OK ] FunctionTest.Powers (0 ms) 44: [ RUN ] FunctionTest.ErfInvFloat 44: [ OK ] FunctionTest.ErfInvFloat (0 ms) 44: [ RUN ] FunctionTest.ErfInvDouble 44: [ OK ] FunctionTest.ErfInvDouble (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 44: [----------] 21 tests from FunctionTest (6 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 44: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 44: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 44: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 44: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 44: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 44: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 44: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 44: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 44: 44: [----------] 4 tests from GaussianOn1DLattice 44: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 44: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 44: [ RUN ] GaussianOn1DLattice.isCorrect 44: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 44: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 44: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 44: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 44: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 44: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 44: 44: [----------] 9 tests from GaussTransformTest 44: [ RUN ] GaussTransformTest.isZeroUponConstruction 44: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 44: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 44: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 44: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 44: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 44: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 44: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 44: [ RUN ] GaussTransformTest.view 44: [ OK ] GaussTransformTest.view (0 ms) 44: [----------] 9 tests from GaussTransformTest (0 ms total) 44: 44: [----------] 3 tests from DensityFittingForce 44: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 44: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 44: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 44: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 44: [ RUN ] DensityFittingForce.pullsTowardsDerivative 44: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 44: [----------] 3 tests from DensityFittingForce (0 ms total) 44: 44: [----------] 2 tests from InvertMatrixTest 44: [ RUN ] InvertMatrixTest.IdentityIsImpotent 44: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertMatrixTest.ComputesInverse 44: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 44: [----------] 2 tests from InvertMatrixTest (0 ms total) 44: 44: [----------] 28 tests from MatrixTest 44: [ RUN ] MatrixTest.canSetFromArray 44: [ OK ] MatrixTest.canSetFromArray (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallyFromList 44: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallySingleValue 44: [ OK ] MatrixTest.canSetStaticallySingleValue (0 ms) 44: [ RUN ] MatrixTest.canConstructAndFill 44: [ OK ] MatrixTest.canConstructAndFill (0 ms) 44: [ RUN ] MatrixTest.canSetValues 44: [ OK ] MatrixTest.canSetValues (0 ms) 44: [ RUN ] MatrixTest.canCopyAssign 44: [ OK ] MatrixTest.canCopyAssign (0 ms) 44: [ RUN ] MatrixTest.canSwap 44: [ OK ] MatrixTest.canSwap (0 ms) 44: [ RUN ] MatrixTest.staticMultiDimArrayExtent 44: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MatrixTest.canAddMatrix 44: [ OK ] MatrixTest.canAddMatrix (0 ms) 44: [ RUN ] MatrixTest.canAddAssignMatrix 44: [ OK ] MatrixTest.canAddAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractMatrix 44: [ OK ] MatrixTest.canSubtractMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractAssignMatrix 44: [ OK ] MatrixTest.canSubtractAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canNegateMatrix 44: [ OK ] MatrixTest.canNegateMatrix (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarMultiplication 44: [ OK ] MatrixTest.MatrixScalarMultiplication (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarDivision 44: [ OK ] MatrixTest.MatrixScalarDivision (0 ms) 44: [ RUN ] MatrixTest.MatrixVectorMultiplicationOperator 44: [ OK ] MatrixTest.MatrixVectorMultiplicationOperator (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 44: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixMultiplication 44: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 44: [ RUN ] MatrixTest.determinantWorks 44: [ OK ] MatrixTest.determinantWorks (0 ms) 44: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 44: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 44: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 44: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 44: [ RUN ] MatrixTest.traceWorks 44: [ OK ] MatrixTest.traceWorks (0 ms) 44: [ RUN ] MatrixTest.transposeWorks 44: [ OK ] MatrixTest.transposeWorks (0 ms) 44: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 44: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 44: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 44: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.canFillLegacyMatrix 44: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.IdentityMatrix 44: [ OK ] MatrixTest.IdentityMatrix (0 ms) 44: [ RUN ] MatrixTest.DiagonalMatrix 44: [ OK ] MatrixTest.DiagonalMatrix (0 ms) 44: [----------] 28 tests from MatrixTest (0 ms total) 44: 44: [----------] 25 tests from MultiDimArrayTest 44: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 44: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 44: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 44: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 44: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 44: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 44: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 44: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 44: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 44: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 44: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 44: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 44: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapStatic 44: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapDynamic 44: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToView 44: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToConstView 44: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 44: [ RUN ] MultiDimArrayTest.viewBegin 44: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.viewEnd 44: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstBegin 44: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstEnd 44: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 44: [----------] 25 tests from MultiDimArrayTest (0 ms total) 44: 44: [----------] 4 tests from MultiDimArrayToMdSpanTest 44: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 44: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 44: 44: [----------] 9 tests from NelderMeadSimplexTest 44: [ RUN ] NelderMeadSimplexTest.BestVertex 44: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.WorstVertex 44: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 44: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 44: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 44: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 44: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 44: [ RUN ] NelderMeadSimplexTest.OrientedLength 44: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 44: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 44: 44: [----------] 2 tests from NelderMead 44: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 44: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (9 ms) 44: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 44: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 44: [----------] 2 tests from NelderMead (9 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ResizeWorks 44: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorks 44: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanCopyAssign 44: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanMoveAssign 44: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanSwap 44: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ResizeWorks 44: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorks 44: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanCopyAssign 44: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanMoveAssign 44: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanSwap 44: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ResizeWorks 44: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorks 44: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanCopyAssign 44: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanMoveAssign 44: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanSwap 44: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ResizeWorks 44: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorks 44: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanCopyAssign 44: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanMoveAssign 44: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanSwap 44: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ResizeWorks 44: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorks 44: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanCopyAssign 44: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanMoveAssign 44: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanSwap 44: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ResizeWorks 44: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorks 44: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanCopyAssign 44: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanMoveAssign 44: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanSwap 44: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ResizeWorks 44: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorks 44: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanCopyAssign 44: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanMoveAssign 44: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanSwap 44: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ResizeWorks 44: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorks 44: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanCopyAssign 44: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanMoveAssign 44: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanSwap 44: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ResizeWorks 44: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorks 44: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanCopyAssign 44: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanMoveAssign 44: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanSwap 44: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ResizeWorks 44: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorks 44: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanCopyAssign 44: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanMoveAssign 44: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanSwap 44: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 293 tests from 40 test suites ran. (51 ms total) 44: [ PASSED ] 293 tests. 44/104 Test #44: MathUnitTests ............................. Passed 0.07 sec test 45 Start 45: MdrunUtilityUnitTests 45: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests 45: Test timeout computed to be: 60 45: [==========] Running 33 tests from 3 test suites. 45: [----------] Global test environment set-up. 45: [----------] 4 tests from MDModulesNotifierTest 45: [ RUN ] MDModulesNotifierTest.AddConsumer 45: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 45: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 45: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 45: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 45: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 45: 45: [----------] 1 test from PlainPairlistRanges 45: [ RUN ] PlainPairlistRanges.RmsdDistance 45: [ OK ] PlainPairlistRanges.RmsdDistance (0 ms) 45: [----------] 1 test from PlainPairlistRanges (0 ms total) 45: 45: [----------] 28 tests from ThreadAffinityTest 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 45: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 45: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 45: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 45: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndFullMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndFullMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask (0 ms) 45: [ RUN ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall 45: [ OK ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithSmt (18 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToECoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem (0 ms) 45: [----------] 28 tests from ThreadAffinityTest (26 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 33 tests from 3 test suites ran. (27 ms total) 45: [ PASSED ] 33 tests. 45/104 Test #45: MdrunUtilityUnitTests ..................... Passed 0.04 sec test 46 Start 46: MdrunUtilityMpiUnitTests 46: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdrunutility/tests 46: Test timeout computed to be: 60 46: [==========] Running 17 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 10 tests from ThreadAffinityMultiRankTest 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 46: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (81 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (56 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 46: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (39 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 46: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (7 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (91 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (44 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent (79 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame (15 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp (64 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken (54 ms) 46: [----------] 10 tests from ThreadAffinityMultiRankTest (536 ms total) 46: 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (48 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (41 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (82 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (55 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (63 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (36 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (91 ms) 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (420 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 17 tests from 2 test suites ran. (957 ms total) 46: [ PASSED ] 17 tests. 46/104 Test #46: MdrunUtilityMpiUnitTests .................. Passed 0.97 sec test 47 Start 47: MDSpanTests 47: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MDSpanTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdspan/tests 47: Test timeout computed to be: 60 47: [==========] Running 32 tests from 7 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from BasicAccessorPolicy 47: [ RUN ] BasicAccessorPolicy.Decay 47: [ OK ] BasicAccessorPolicy.Decay (0 ms) 47: [ RUN ] BasicAccessorPolicy.Access 47: [ OK ] BasicAccessorPolicy.Access (0 ms) 47: [ RUN ] BasicAccessorPolicy.Offset 47: [ OK ] BasicAccessorPolicy.Offset (0 ms) 47: [ RUN ] BasicAccessorPolicy.CopyAccessor 47: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 47: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 47: 47: [----------] 4 tests from ExtentsTest 47: [ RUN ] ExtentsTest.Construction 47: [ OK ] ExtentsTest.Construction (0 ms) 47: [ RUN ] ExtentsTest.PurelyStatic 47: [ OK ] ExtentsTest.PurelyStatic (0 ms) 47: [ RUN ] ExtentsTest.RankNought 47: [ OK ] ExtentsTest.RankNought (0 ms) 47: [ RUN ] ExtentsTest.Assignment 47: [ OK ] ExtentsTest.Assignment (0 ms) 47: [----------] 4 tests from ExtentsTest (0 ms total) 47: 47: [----------] 8 tests from MdSpanExtension 47: [ RUN ] MdSpanExtension.SlicingAllStatic 47: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingDynamic 47: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingAllStatic3D 47: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 47: [ RUN ] MdSpanExtension.SlicingEqualsView3D 47: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 47: [ RUN ] MdSpanExtension.additionWorks 47: [ OK ] MdSpanExtension.additionWorks (0 ms) 47: [ RUN ] MdSpanExtension.subtractionWorks 47: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 47: [ RUN ] MdSpanExtension.multiplicationWorks 47: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 47: [ RUN ] MdSpanExtension.divisionWorks 47: [ OK ] MdSpanExtension.divisionWorks (0 ms) 47: [----------] 8 tests from MdSpanExtension (0 ms total) 47: 47: [----------] 3 tests from LayoutTests 47: [ RUN ] LayoutTests.LayoutRightConstruction 47: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 47: [ RUN ] LayoutTests.LayoutRightProperties 47: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 47: [ RUN ] LayoutTests.LayoutRightOperator 47: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 47: [----------] 3 tests from LayoutTests (0 ms total) 47: 47: [----------] 1 test from MdSpanTest 47: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 47: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 47: [----------] 1 test from MdSpanTest (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/0.Rank 47: [ OK ] MdSpanTest/0.Rank (0 ms) 47: [ RUN ] MdSpanTest/0.DynamicRank 47: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/0.Extents 47: [ OK ] MdSpanTest/0.Extents (0 ms) 47: [ RUN ] MdSpanTest/0.Strides 47: [ OK ] MdSpanTest/0.Strides (0 ms) 47: [ RUN ] MdSpanTest/0.Properties 47: [ OK ] MdSpanTest/0.Properties (0 ms) 47: [ RUN ] MdSpanTest/0.Operator 47: [ OK ] MdSpanTest/0.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/0 (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/1.Rank 47: [ OK ] MdSpanTest/1.Rank (0 ms) 47: [ RUN ] MdSpanTest/1.DynamicRank 47: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/1.Extents 47: [ OK ] MdSpanTest/1.Extents (0 ms) 47: [ RUN ] MdSpanTest/1.Strides 47: [ OK ] MdSpanTest/1.Strides (0 ms) 47: [ RUN ] MdSpanTest/1.Properties 47: [ OK ] MdSpanTest/1.Properties (0 ms) 47: [ RUN ] MdSpanTest/1.Operator 47: [ OK ] MdSpanTest/1.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/1 (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 32 tests from 7 test suites ran. (0 ms total) 47: [ PASSED ] 32 tests. 47/104 Test #47: MDSpanTests ............................... Passed 0.01 sec test 48 Start 48: MdtypesUnitTest 48: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/mdtypes/tests 48: Test timeout computed to be: 60 48: [==========] Running 98 tests from 7 test suites. 48: [----------] Global test environment set-up. 48: [----------] 4 tests from ForeingLambdaTermsDhdl 48: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 48: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 48: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 48: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 48: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 48: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 48: 48: [----------] 4 tests from ObservablesReducerTest 48: [ RUN ] ObservablesReducerTest.CanMoveAssign 48: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 48: [ RUN ] ObservablesReducerTest.CanMoveConstruct 48: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 48: [----------] 4 tests from ObservablesReducerTest (0 ms total) 48: 48: [----------] 3 tests from CheckpointDataTest 48: [ RUN ] CheckpointDataTest.SingleDataTest 48: [ OK ] CheckpointDataTest.SingleDataTest (2 ms) 48: [ RUN ] CheckpointDataTest.MultiDataTest 48: [ OK ] CheckpointDataTest.MultiDataTest (13 ms) 48: [ RUN ] CheckpointDataTest.EmptyVectorTest 48: [ OK ] CheckpointDataTest.EmptyVectorTest (0 ms) 48: [----------] 3 tests from CheckpointDataTest (16 ms total) 48: 48: [----------] 7 tests from ForceBuffers 48: [ RUN ] ForceBuffers.ConstructsUnpinned 48: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsPinned 48: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsEmpty 48: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 48: [ RUN ] ForceBuffers.ResizeWorks 48: [ OK ] ForceBuffers.ResizeWorks (0 ms) 48: [ RUN ] ForceBuffers.PaddingWorks 48: [ OK ] ForceBuffers.PaddingWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyWorks 48: [ OK ] ForceBuffers.CopyWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyDoesNotPin 48: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 48: [----------] 7 tests from ForceBuffers (0 ms total) 48: 48: [----------] 5 tests from MultipleTimeStepping 48: [ RUN ] MultipleTimeStepping.ChecksNumLevels 48: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 48: [ RUN ] MultipleTimeStepping.SelectsForceGroups 48: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksStepFactor 48: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 48: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksIntegrator 48: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 48: [----------] 5 tests from MultipleTimeStepping (0 ms total) 48: 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 48: 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 98 tests from 7 test suites ran. (16 ms total) 48: [ PASSED ] 98 tests. 48/104 Test #48: MdtypesUnitTest ........................... Passed 0.03 sec test 49 Start 49: OnlineHelpUnitTests 49: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/onlinehelp/tests 49: Test timeout computed to be: 60 49: [==========] Running 22 tests from 4 test suites. 49: [----------] Global test environment set-up. 49: [----------] 6 tests from TextTableFormatterTest 49: [ RUN ] TextTableFormatterTest.HandlesBasicCase 49: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesIndentation 49: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 49: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 49: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 49: [----------] 6 tests from TextTableFormatterTest (2 ms total) 49: 49: [----------] 3 tests from HelpManagerTest 49: [ RUN ] HelpManagerTest.HandlesRootTopic 49: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 49: [ RUN ] HelpManagerTest.HandlesSubTopics 49: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 49: [ RUN ] HelpManagerTest.HandlesInvalidTopics 49: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 49: [----------] 3 tests from HelpManagerTest (1 ms total) 49: 49: [----------] 2 tests from HelpTopicFormattingTest 49: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 49: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 49: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 49: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 49: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 49: 49: [----------] 11 tests from HelpWriterContextTest 49: [ RUN ] HelpWriterContextTest.FormatsParagraphs 49: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 49: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 49: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralText 49: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsBulletList 49: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 49: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 49: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsGridTable 49: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsTitles 49: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 49: [----------] 11 tests from HelpWriterContextTest (4 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 22 tests from 4 test suites ran. (10 ms total) 49: [ PASSED ] 22 tests. 49/104 Test #49: OnlineHelpUnitTests ....................... Passed 0.02 sec test 50 Start 50: OptionsUnitTests 50: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/OptionsUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/options/tests 50: Test timeout computed to be: 60 50: [==========] Running 151 tests from 21 test suites. 50: [----------] Global test environment set-up. 50: [----------] 5 tests from AbstractOptionStorageTest 50: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 50: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 50: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 50: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 50: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 50: 50: [----------] 10 tests from FileNameOptionTest 50: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 50: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 50: [----------] 10 tests from FileNameOptionTest (1 ms total) 50: 50: [----------] 16 tests from FileNameOptionManagerTest 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 50: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 50: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 50: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 50: 50: [----------] 1 test from OptionsTest 50: [ RUN ] OptionsTest.FailsOnNonsafeStorage 50: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 50: [----------] 1 test from OptionsTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerTest 50: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 50: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 50: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMissingValue 50: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesExtraValue 50: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesGroups 50: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesSections 50: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 50: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 50: [----------] 9 tests from OptionsAssignerTest (0 ms total) 50: 50: [----------] 4 tests from OptionsAssignerBooleanTest 50: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 50: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 50: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 50: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 50: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 50: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerIntegerTest 50: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerInt64Test 50: [ RUN ] OptionsAssignerInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresToVector 50: [ OK ] OptionsAssignerInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerInt64Test (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresToVector 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test (0 ms total) 50: 50: [----------] 5 tests from OptionsAssignerDoubleTest 50: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 50: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 50: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 50: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerStringTest 50: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 50: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 50: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 50: 50: [----------] 6 tests from OptionsAssignerEnumTest 50: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 50: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 50: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 50: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 50: 50: [----------] 8 tests from RepeatingOptionSectionTest 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 50: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 50: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 50: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 50: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 50: 50: [----------] 1 test from TimeUnitManagerTest 50: [ RUN ] TimeUnitManagerTest.BasicOperations 50: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 50: [----------] 1 test from TimeUnitManagerTest (0 ms total) 50: 50: [----------] 4 tests from TimeUnitBehaviorTest 50: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 50: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 50: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 50: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 50: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 50: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 50: 50: [----------] 2 tests from TreeValueSupportAssignTest 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 50: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 50: 50: [----------] 1 test from TreeValueSupportAssignErrorTest 50: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 50: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 50: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 50: 50: [----------] 5 tests from TreeValueSupportCheckTest 50: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 50: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 50: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 50: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 50: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 50: 50: [----------] 6 tests from TreeValueSupportAdjustTest 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms) 50: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 50: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 50: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 50: [----------] 6 tests from TreeValueSupportAdjustTest (5 ms total) 50: 50: [----------] 7 tests from TreeValueSupportTest 50: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 50: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 50: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsInt64Option 50: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsStringOption 50: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsFloatOption 50: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 50: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsEnumOption 50: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 50: [----------] 7 tests from TreeValueSupportTest (3 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 151 tests from 21 test suites ran. (15 ms total) 50: [ PASSED ] 151 tests. 50/104 Test #50: OptionsUnitTests .......................... Passed 0.03 sec test 51 Start 51: PbcutilUnitTest 51: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 51: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pbcutil/tests 51: Test timeout computed to be: 60 51: [==========] Running 37 tests from 5 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ShiftTest 51: [ RUN ] ShiftTest.CoordinateShiftWorks 51: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 51: [----------] 1 test from ShiftTest (0 ms total) 51: 51: [----------] 2 tests from MShift 51: [ RUN ] MShift.shiftsAndUnshifts 51: [ OK ] MShift.shiftsAndUnshifts (0 ms) 51: [ RUN ] MShift.shiftsAndUnshiftsSelf 51: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 51: [----------] 2 tests from MShift (0 ms total) 51: 51: [----------] 5 tests from PbcTest 51: [ RUN ] PbcTest.CalcShiftsWorks 51: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 51: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 51: [----------] 5 tests from PbcTest (0 ms total) 51: 51: [----------] 2 tests from PbcEnumsTest 51: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 51: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 51: [----------] 2 tests from PbcEnumsTest (0 ms total) 51: 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (14 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 37 tests from 5 test suites ran. (15 ms total) 51: [ PASSED ] 37 tests. 51/104 Test #51: PbcutilUnitTest ........................... Passed 0.03 sec test 52 Start 52: RandomUnitTests 52: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/RandomUnitTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/random/tests 52: Test timeout computed to be: 60 52: [==========] Running 44 tests from 10 test suites. 52: [----------] Global test environment set-up. 52: [----------] 4 tests from ExponentialDistributionTest 52: [ RUN ] ExponentialDistributionTest.Output 52: [ OK ] ExponentialDistributionTest.Output (1 ms) 52: [ RUN ] ExponentialDistributionTest.Logical 52: [ OK ] ExponentialDistributionTest.Logical (0 ms) 52: [ RUN ] ExponentialDistributionTest.Reset 52: [ OK ] ExponentialDistributionTest.Reset (0 ms) 52: [ RUN ] ExponentialDistributionTest.AltParam 52: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from ExponentialDistributionTest (1 ms total) 52: 52: [----------] 4 tests from GammaDistributionTest 52: [ RUN ] GammaDistributionTest.Output 52: [ OK ] GammaDistributionTest.Output (0 ms) 52: [ RUN ] GammaDistributionTest.Logical 52: [ OK ] GammaDistributionTest.Logical (0 ms) 52: [ RUN ] GammaDistributionTest.Reset 52: [ OK ] GammaDistributionTest.Reset (0 ms) 52: [ RUN ] GammaDistributionTest.AltParam 52: [ OK ] GammaDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from GammaDistributionTest (0 ms total) 52: 52: [----------] 4 tests from NormalDistributionTest 52: [ RUN ] NormalDistributionTest.Output 52: [ OK ] NormalDistributionTest.Output (0 ms) 52: [ RUN ] NormalDistributionTest.Logical 52: [ OK ] NormalDistributionTest.Logical (0 ms) 52: [ RUN ] NormalDistributionTest.Reset 52: [ OK ] NormalDistributionTest.Reset (0 ms) 52: [ RUN ] NormalDistributionTest.AltParam 52: [ OK ] NormalDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from NormalDistributionTest (0 ms total) 52: 52: [----------] 1 test from SeedTest 52: [ RUN ] SeedTest.makeRandomSeed 52: [ OK ] SeedTest.makeRandomSeed (0 ms) 52: [----------] 1 test from SeedTest (0 ms total) 52: 52: [----------] 6 tests from TabulatedNormalDistributionTest 52: [ RUN ] TabulatedNormalDistributionTest.Output14 52: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Output16 52: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 52: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Logical 52: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Reset 52: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.AltParam 52: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 52: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 52: 52: [----------] 1 test from TabulatedNormalDistributionTableTest 52: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 52: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 52: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 52: 52: [----------] 6 tests from ThreeFry2x64Test 52: [ RUN ] ThreeFry2x64Test.Logical 52: [ OK ] ThreeFry2x64Test.Logical (0 ms) 52: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 52: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 52: [ RUN ] ThreeFry2x64Test.Reseed 52: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 52: [ RUN ] ThreeFry2x64Test.Discard 52: [ OK ] ThreeFry2x64Test.Discard (0 ms) 52: [ RUN ] ThreeFry2x64Test.InvalidCounter 52: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 52: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 52: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 52: [----------] 6 tests from ThreeFry2x64Test (2 ms total) 52: 52: [----------] 4 tests from UniformIntDistributionTest 52: [ RUN ] UniformIntDistributionTest.Output 52: [ OK ] UniformIntDistributionTest.Output (0 ms) 52: [ RUN ] UniformIntDistributionTest.Logical 52: [ OK ] UniformIntDistributionTest.Logical (0 ms) 52: [ RUN ] UniformIntDistributionTest.Reset 52: [ OK ] UniformIntDistributionTest.Reset (0 ms) 52: [ RUN ] UniformIntDistributionTest.AltParam 52: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from UniformIntDistributionTest (1 ms total) 52: 52: [----------] 5 tests from UniformRealDistributionTest 52: [ RUN ] UniformRealDistributionTest.GenerateCanonical 52: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Output 52: [ OK ] UniformRealDistributionTest.Output (0 ms) 52: [ RUN ] UniformRealDistributionTest.Logical 52: [ OK ] UniformRealDistributionTest.Logical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Reset 52: [ OK ] UniformRealDistributionTest.Reset (0 ms) 52: [ RUN ] UniformRealDistributionTest.AltParam 52: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 52: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 52: 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (3 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (8 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 44 tests from 10 test suites ran. (17 ms total) 52: [ PASSED ] 44 tests. 52/104 Test #52: RandomUnitTests ........................... Passed 0.03 sec test 53 Start 53: RestraintTests 53: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/RestraintTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/restraint/tests 53: Test timeout computed to be: 60 53: [==========] Running 1 test from 1 test suite. 53: [----------] Global test environment set-up. 53: [----------] 1 test from RestraintManager 53: [ RUN ] RestraintManager.restraintList 53: [ OK ] RestraintManager.restraintList (0 ms) 53: [----------] 1 test from RestraintManager (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 1 test from 1 test suite ran. (0 ms total) 53: [ PASSED ] 1 test. 53/104 Test #53: RestraintTests ............................ Passed 0.01 sec test 54 Start 54: SerializationUnitTests 54: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/serialization-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/SerializationUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/serialization/tests 54: Test timeout computed to be: 60 54: [==========] Running 9 tests from 2 test suites. 54: [----------] Global test environment set-up. 54: [----------] 5 tests from InMemorySerializerTest 54: [ RUN ] InMemorySerializerTest.Roundtrip 54: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 54: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 54: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SizeIsCorrect 54: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 54: [----------] 5 tests from InMemorySerializerTest (0 ms total) 54: 54: [----------] 4 tests from KeyValueTreeSerializerTest 54: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 54: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms) 54: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 54: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms) 54: [----------] 4 tests from KeyValueTreeSerializerTest (3 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 9 tests from 2 test suites ran. (4 ms total) 54: [ PASSED ] 9 tests. 54/104 Test #54: SerializationUnitTests .................... Passed 0.02 sec test 55 Start 55: TableUnitTests 55: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/TableUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tables/tests 55: Test timeout computed to be: 60 55: [==========] Running 20 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 55: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/0.Sinc 55: [ OK ] SplineTableTest/0.Sinc (0 ms) 55: [ RUN ] SplineTableTest/0.LJ12 55: [ OK ] SplineTableTest/0.LJ12 (8 ms) 55: [ RUN ] SplineTableTest/0.PmeCorrection 55: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/0.TwoFunctions 55: [ OK ] SplineTableTest/0.TwoFunctions (14 ms) 55: [ RUN ] SplineTableTest/0.ThreeFunctions 55: [ OK ] SplineTableTest/0.ThreeFunctions (14 ms) 55: [ RUN ] SplineTableTest/0.Simd 55: [ OK ] SplineTableTest/0.Simd (2 ms) 55: [ RUN ] SplineTableTest/0.SimdTwoFunctions 55: [ OK ] SplineTableTest/0.SimdTwoFunctions (10 ms) 55: [----------] 10 tests from SplineTableTest/0 (54 ms total) 55: 55: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 55: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/1.Sinc 55: [ OK ] SplineTableTest/1.Sinc (0 ms) 55: [ RUN ] SplineTableTest/1.LJ12 55: [ OK ] SplineTableTest/1.LJ12 (0 ms) 55: [ RUN ] SplineTableTest/1.PmeCorrection 55: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/1.TwoFunctions 55: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 55: [ RUN ] SplineTableTest/1.ThreeFunctions 55: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 55: [ RUN ] SplineTableTest/1.Simd 55: [ OK ] SplineTableTest/1.Simd (0 ms) 55: [ RUN ] SplineTableTest/1.SimdTwoFunctions 55: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 55: [----------] 10 tests from SplineTableTest/1 (7 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 20 tests from 2 test suites ran. (62 ms total) 55: [ PASSED ] 20 tests. 55/104 Test #55: TableUnitTests ............................ Passed 0.08 sec test 56 Start 56: TaskAssignmentUnitTests 56: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/taskassignment/tests 56: Test timeout computed to be: 60 56: [==========] Running 3 tests from 2 test suites. 56: [----------] Global test environment set-up. 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 56: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 56: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 56: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 56: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 56: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 56: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 3 tests from 2 test suites ran. (0 ms total) 56: [ PASSED ] 3 tests. 56/104 Test #56: TaskAssignmentUnitTests ................... Passed 0.01 sec test 57 Start 57: GmxTimingTests 57: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GmxTimingTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/timing/tests 57: Test timeout computed to be: 60 57: [==========] Running 6 tests from 1 test suite. 57: [----------] Global test environment set-up. 57: [----------] 6 tests from TimingTest 57: [ RUN ] TimingTest.ElementCountingWorks 57: [ OK ] TimingTest.ElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.ElementNoCountingWorks 57: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementCountingWorks 57: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementNoCountingWorks 57: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.RunWallCycle 57: [ OK ] TimingTest.RunWallCycle (1 ms) 57: [ RUN ] TimingTest.RunWallCycleSub 57: [ OK ] TimingTest.RunWallCycleSub (0 ms) 57: [----------] 6 tests from TimingTest (1 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 6 tests from 1 test suite ran. (1 ms total) 57: [ PASSED ] 6 tests. 57/104 Test #57: GmxTimingTests ............................ Passed 0.05 sec test 58 Start 58: TopologyTest 58: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/TopologyTest.xml" 58: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/topology/tests 58: Test timeout computed to be: 60 58: [==========] Running 153 tests from 10 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from PdbAtomEntryTest 58: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 58: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 58: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 58: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 58: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 58: 58: [----------] 3 tests from ExclusionBlockTest 58: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 58: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 58: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 58: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 58: [ RUN ] ExclusionBlockTest.MergeExclusions 58: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 58: [----------] 3 tests from ExclusionBlockTest (0 ms total) 58: 58: [----------] 6 tests from InteractionListTest 58: [ RUN ] InteractionListTest.EmptyWorks 58: [ OK ] InteractionListTest.EmptyWorks (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArray 58: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 58: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionPointer 58: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 58: [ RUN ] InteractionListTest.CanAddListToOtherList 58: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 58: [ RUN ] InteractionListTest.ClearingWorks 58: [ OK ] InteractionListTest.ClearingWorks (0 ms) 58: [----------] 6 tests from InteractionListTest (0 ms total) 58: 58: [----------] 3 tests from IndexTest 58: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.AnalyseWorksDefaultGroups (8 ms) 58: [ RUN ] IndexTest.WriteIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteIndexWorks (2 ms) 58: [ RUN ] IndexTest.WriteAndReadIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteAndReadIndexWorks (2 ms) 58: [----------] 3 tests from IndexTest (14 ms total) 58: 58: [----------] 4 tests from MtopTest 58: [ RUN ] MtopTest.RangeBasedLoop 58: [ OK ] MtopTest.RangeBasedLoop (0 ms) 58: [ RUN ] MtopTest.Operators 58: [ OK ] MtopTest.Operators (0 ms) 58: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 58: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 58: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 58: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 58: [----------] 4 tests from MtopTest (0 ms total) 58: 58: [----------] 2 tests from IListRangeTest 58: [ RUN ] IListRangeTest.RangeBasedLoopWorks 58: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 58: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 58: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 58: [----------] 2 tests from IListRangeTest (0 ms total) 58: 58: [----------] 13 tests from StringTableTest 58: [ RUN ] StringTableTest.AddSingleEntry 58: [ OK ] StringTableTest.AddSingleEntry (0 ms) 58: [ RUN ] StringTableTest.CanAccessWithAt 58: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 58: [ RUN ] StringTableTest.CanAccessWithBracket 58: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 58: [ RUN ] StringTableTest.ThrowsOutOfRange 58: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 58: [ RUN ] StringTableTest.StringCompareIsCorrect 58: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 58: [ RUN ] StringTableTest.AddTwoDistinctEntries 58: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] StringTableTest.TryToAddDuplicates 58: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 58: [ RUN ] StringTableTest.AddLargeNumberOfEntries 58: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 58: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 58: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 58: [ RUN ] StringTableTest.CanWriteToBuffer 58: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 58: [ RUN ] StringTableTest.Roundtrip 58: [ OK ] StringTableTest.Roundtrip (0 ms) 58: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 58: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 58: [ RUN ] StringTableTest.CanCopyToLegacyTable 58: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 58: [----------] 13 tests from StringTableTest (6 ms total) 58: 58: [----------] 6 tests from LegacySymtabTest 58: [ RUN ] LegacySymtabTest.EmptyOnOpen 58: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 58: [ RUN ] LegacySymtabTest.AddSingleEntry 58: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 58: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 58: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] LegacySymtabTest.TryToAddDuplicates 58: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 58: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 58: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 58: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 58: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 58: [----------] 6 tests from LegacySymtabTest (0 ms total) 58: 58: [----------] 5 tests from TopSortTest 58: [ RUN ] TopSortTest.WorksOnEmptyIdef 58: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 58: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 58: [----------] 5 tests from TopSortTest (0 ms total) 58: 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (48 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 153 tests from 10 test suites ran. (70 ms total) 58: [ PASSED ] 153 tests. 58: 58: YOU HAVE 1 DISABLED TEST 58: 58/104 Test #58: TopologyTest .............................. Passed 0.09 sec test 59 Start 59: PullTest 59: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/PullTest.xml" 59: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/pulling/tests 59: Test timeout computed to be: 60 59: [==========] Running 10 tests from 1 test suite. 59: [----------] Global test environment set-up. 59: [----------] 10 tests from PullTest 59: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 59: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 59: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 59: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 59: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 59: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 59: [ RUN ] PullTest.TransformationCoordSimple 59: [ OK ] PullTest.TransformationCoordSimple (0 ms) 59: [ RUN ] PullTest.TransformationCoordAdvanced 59: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 59: [ RUN ] PullTest.TransformationCoordTime 59: [ OK ] PullTest.TransformationCoordTime (0 ms) 59: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 59: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 59: [ RUN ] PullTest.TransformationCoordDummyExpression 59: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 59: [----------] 10 tests from PullTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 10 tests from 1 test suite ran. (1 ms total) 59: [ PASSED ] 10 tests. 59/104 Test #59: PullTest .................................. Passed 0.02 sec test 60 Start 60: SimdUnitTests 60: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/SimdUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/simd/tests 60: Test timeout computed to be: 60 60: [==========] Running 288 tests from 22 test suites. 60: [----------] Global test environment set-up. 60: [----------] 9 tests from SimdBootstrapTest 60: [ RUN ] SimdBootstrapTest.loadStore 60: [ OK ] SimdBootstrapTest.loadStore (0 ms) 60: [ RUN ] SimdBootstrapTest.loadU 60: [ OK ] SimdBootstrapTest.loadU (0 ms) 60: [ RUN ] SimdBootstrapTest.storeU 60: [ OK ] SimdBootstrapTest.storeU (0 ms) 60: [ RUN ] SimdBootstrapTest.loadStoreI 60: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 60: [ RUN ] SimdBootstrapTest.loadUI 60: [ OK ] SimdBootstrapTest.loadUI (0 ms) 60: [ RUN ] SimdBootstrapTest.storeUI 60: [ OK ] SimdBootstrapTest.storeUI (0 ms) 60: [ RUN ] SimdBootstrapTest.simd4LoadStore 60: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 60: [ RUN ] SimdBootstrapTest.simd4LoadU 60: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 60: [ RUN ] SimdBootstrapTest.simd4StoreU 60: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 60: [----------] 9 tests from SimdBootstrapTest (0 ms total) 60: 60: [----------] 41 tests from SimdScalarTest 60: [ RUN ] SimdScalarTest.load 60: [ OK ] SimdScalarTest.load (0 ms) 60: [ RUN ] SimdScalarTest.loadU 60: [ OK ] SimdScalarTest.loadU (0 ms) 60: [ RUN ] SimdScalarTest.store 60: [ OK ] SimdScalarTest.store (0 ms) 60: [ RUN ] SimdScalarTest.storeU 60: [ OK ] SimdScalarTest.storeU (0 ms) 60: [ RUN ] SimdScalarTest.setZero 60: [ OK ] SimdScalarTest.setZero (0 ms) 60: [ RUN ] SimdScalarTest.andNot 60: [ OK ] SimdScalarTest.andNot (0 ms) 60: [ RUN ] SimdScalarTest.fma 60: [ OK ] SimdScalarTest.fma (0 ms) 60: [ RUN ] SimdScalarTest.fms 60: [ OK ] SimdScalarTest.fms (0 ms) 60: [ RUN ] SimdScalarTest.fnma 60: [ OK ] SimdScalarTest.fnma (0 ms) 60: [ RUN ] SimdScalarTest.fnms 60: [ OK ] SimdScalarTest.fnms (0 ms) 60: [ RUN ] SimdScalarTest.maskAdd 60: [ OK ] SimdScalarTest.maskAdd (0 ms) 60: [ RUN ] SimdScalarTest.maskzMul 60: [ OK ] SimdScalarTest.maskzMul (0 ms) 60: [ RUN ] SimdScalarTest.maskzFma 60: [ OK ] SimdScalarTest.maskzFma (0 ms) 60: [ RUN ] SimdScalarTest.abs 60: [ OK ] SimdScalarTest.abs (0 ms) 60: [ RUN ] SimdScalarTest.max 60: [ OK ] SimdScalarTest.max (0 ms) 60: [ RUN ] SimdScalarTest.min 60: [ OK ] SimdScalarTest.min (0 ms) 60: [ RUN ] SimdScalarTest.round 60: [ OK ] SimdScalarTest.round (0 ms) 60: [ RUN ] SimdScalarTest.trunc 60: [ OK ] SimdScalarTest.trunc (0 ms) 60: [ RUN ] SimdScalarTest.reduce 60: [ OK ] SimdScalarTest.reduce (0 ms) 60: [ RUN ] SimdScalarTest.testBits 60: [ OK ] SimdScalarTest.testBits (0 ms) 60: [ RUN ] SimdScalarTest.anyTrue 60: [ OK ] SimdScalarTest.anyTrue (0 ms) 60: [ RUN ] SimdScalarTest.selectByMask 60: [ OK ] SimdScalarTest.selectByMask (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMask 60: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 60: [ RUN ] SimdScalarTest.blend 60: [ OK ] SimdScalarTest.blend (0 ms) 60: [ RUN ] SimdScalarTest.cvtR2I 60: [ OK ] SimdScalarTest.cvtR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvttR2I 60: [ OK ] SimdScalarTest.cvttR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvtI2R 60: [ OK ] SimdScalarTest.cvtI2R (0 ms) 60: [ RUN ] SimdScalarTest.cvtF2D 60: [ OK ] SimdScalarTest.cvtF2D (0 ms) 60: [ RUN ] SimdScalarTest.cvtD2D 60: [ OK ] SimdScalarTest.cvtD2D (0 ms) 60: [ RUN ] SimdScalarTest.loadI 60: [ OK ] SimdScalarTest.loadI (0 ms) 60: [ RUN ] SimdScalarTest.loadUI 60: [ OK ] SimdScalarTest.loadUI (0 ms) 60: [ RUN ] SimdScalarTest.storeI 60: [ OK ] SimdScalarTest.storeI (0 ms) 60: [ RUN ] SimdScalarTest.storeUI 60: [ OK ] SimdScalarTest.storeUI (0 ms) 60: [ RUN ] SimdScalarTest.andNotI 60: [ OK ] SimdScalarTest.andNotI (0 ms) 60: [ RUN ] SimdScalarTest.testBitsI 60: [ OK ] SimdScalarTest.testBitsI (0 ms) 60: [ RUN ] SimdScalarTest.selectByMaskI 60: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMaskI 60: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 60: [ RUN ] SimdScalarTest.blendI 60: [ OK ] SimdScalarTest.blendI (0 ms) 60: [ RUN ] SimdScalarTest.cvtB2IB 60: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 60: [ RUN ] SimdScalarTest.cvtIB2B 60: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 60: [ RUN ] SimdScalarTest.expandScalarsToTriplets 60: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 60: [----------] 41 tests from SimdScalarTest (0 ms total) 60: 60: [----------] 8 tests from SimdScalarUtilTest 60: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 60: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 60: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 60: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 60: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 60: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 60: 60: [----------] 37 tests from SimdScalarMathTest 60: [ RUN ] SimdScalarMathTest.copysign 60: [ OK ] SimdScalarMathTest.copysign (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPair 60: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 60: [ RUN ] SimdScalarMathTest.inv 60: [ OK ] SimdScalarMathTest.inv (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrt 60: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdScalarMathTest.log 60: [ OK ] SimdScalarMathTest.log (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2 60: [ OK ] SimdScalarMathTest.exp2 (0 ms) 60: [ RUN ] SimdScalarMathTest.exp 60: [ OK ] SimdScalarMathTest.exp (0 ms) 60: [ RUN ] SimdScalarMathTest.erf 60: [ OK ] SimdScalarMathTest.erf (0 ms) 60: [ RUN ] SimdScalarMathTest.erfc 60: [ OK ] SimdScalarMathTest.erfc (0 ms) 60: [ RUN ] SimdScalarMathTest.sincos 60: [ OK ] SimdScalarMathTest.sincos (0 ms) 60: [ RUN ] SimdScalarMathTest.sin 60: [ OK ] SimdScalarMathTest.sin (0 ms) 60: [ RUN ] SimdScalarMathTest.cos 60: [ OK ] SimdScalarMathTest.cos (0 ms) 60: [ RUN ] SimdScalarMathTest.tan 60: [ OK ] SimdScalarMathTest.tan (0 ms) 60: [ RUN ] SimdScalarMathTest.asin 60: [ OK ] SimdScalarMathTest.asin (0 ms) 60: [ RUN ] SimdScalarMathTest.acos 60: [ OK ] SimdScalarMathTest.acos (0 ms) 60: [ RUN ] SimdScalarMathTest.atan 60: [ OK ] SimdScalarMathTest.atan (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2 60: [ OK ] SimdScalarMathTest.atan2 (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrection 60: [ OK ] SimdScalarMathTest.pmeForceCorrection (1 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 60: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.invSingleAccuracy 60: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 60: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.logSingleAccuracy 60: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 60: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.expSingleAccuracy 60: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 60: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 60: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 60: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 60: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 60: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 60: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 60: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 60: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 37 tests from SimdScalarMathTest (4 ms total) 60: 60: [----------] 1 test from SimdTest 60: [ RUN ] SimdTest.GmxAligned 60: [ OK ] SimdTest.GmxAligned (0 ms) 60: [----------] 1 test from SimdTest (0 ms total) 60: 60: [----------] 42 tests from SimdFloatingpointTest 60: [ RUN ] SimdFloatingpointTest.setZero 60: [ OK ] SimdFloatingpointTest.setZero (3 ms) 60: [ RUN ] SimdFloatingpointTest.set 60: [ OK ] SimdFloatingpointTest.set (0 ms) 60: [ RUN ] SimdFloatingpointTest.add 60: [ OK ] SimdFloatingpointTest.add (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskAdd 60: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 60: [ RUN ] SimdFloatingpointTest.sub 60: [ OK ] SimdFloatingpointTest.sub (0 ms) 60: [ RUN ] SimdFloatingpointTest.mul 60: [ OK ] SimdFloatingpointTest.mul (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzMul 60: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 60: [ RUN ] SimdFloatingpointTest.fma 60: [ OK ] SimdFloatingpointTest.fma (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzFma 60: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fms 60: [ OK ] SimdFloatingpointTest.fms (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnma 60: [ OK ] SimdFloatingpointTest.fnma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnms 60: [ OK ] SimdFloatingpointTest.fnms (0 ms) 60: [ RUN ] SimdFloatingpointTest.abs 60: [ OK ] SimdFloatingpointTest.abs (0 ms) 60: [ RUN ] SimdFloatingpointTest.neg 60: [ OK ] SimdFloatingpointTest.neg (0 ms) 60: [ RUN ] SimdFloatingpointTest.and 60: [ OK ] SimdFloatingpointTest.and (0 ms) 60: [ RUN ] SimdFloatingpointTest.or 60: [ OK ] SimdFloatingpointTest.or (0 ms) 60: [ RUN ] SimdFloatingpointTest.xor 60: [ OK ] SimdFloatingpointTest.xor (0 ms) 60: [ RUN ] SimdFloatingpointTest.andNot 60: [ OK ] SimdFloatingpointTest.andNot (0 ms) 60: [ RUN ] SimdFloatingpointTest.max 60: [ OK ] SimdFloatingpointTest.max (0 ms) 60: [ RUN ] SimdFloatingpointTest.min 60: [ OK ] SimdFloatingpointTest.min (0 ms) 60: [ RUN ] SimdFloatingpointTest.round 60: [ OK ] SimdFloatingpointTest.round (0 ms) 60: [ RUN ] SimdFloatingpointTest.roundMode 60: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 60: [ RUN ] SimdFloatingpointTest.trunc 60: [ OK ] SimdFloatingpointTest.trunc (0 ms) 60: [ RUN ] SimdFloatingpointTest.frexp 60: [ OK ] SimdFloatingpointTest.frexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.ldexp 60: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.rsqrt 60: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRsqrt 60: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.rcp 60: [ OK ] SimdFloatingpointTest.rcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRcp 60: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 60: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.selectByNotMask 60: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpNe 60: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLe 60: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLt 60: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 60: [ RUN ] SimdFloatingpointTest.testBits 60: [ OK ] SimdFloatingpointTest.testBits (0 ms) 60: [ RUN ] SimdFloatingpointTest.andB 60: [ OK ] SimdFloatingpointTest.andB (0 ms) 60: [ RUN ] SimdFloatingpointTest.orB 60: [ OK ] SimdFloatingpointTest.orB (0 ms) 60: [ RUN ] SimdFloatingpointTest.anyTrueB 60: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 60: [ RUN ] SimdFloatingpointTest.blend 60: [ OK ] SimdFloatingpointTest.blend (0 ms) 60: [ RUN ] SimdFloatingpointTest.reduce 60: [ OK ] SimdFloatingpointTest.reduce (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 60: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 60: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 60: [----------] 42 tests from SimdFloatingpointTest (4 ms total) 60: 60: [----------] 16 tests from SimdFloatingpointUtilTest 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 60: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 60: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 60: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 60: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 60: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 60: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 60: 60: [----------] 23 tests from SimdIntegerTest 60: [ RUN ] SimdIntegerTest.setZero 60: [ OK ] SimdIntegerTest.setZero (0 ms) 60: [ RUN ] SimdIntegerTest.set 60: [ OK ] SimdIntegerTest.set (0 ms) 60: [ RUN ] SimdIntegerTest.add 60: [ OK ] SimdIntegerTest.add (0 ms) 60: [ RUN ] SimdIntegerTest.sub 60: [ OK ] SimdIntegerTest.sub (0 ms) 60: [ RUN ] SimdIntegerTest.mul 60: [ OK ] SimdIntegerTest.mul (0 ms) 60: [ RUN ] SimdIntegerTest.and 60: [ OK ] SimdIntegerTest.and (0 ms) 60: [ RUN ] SimdIntegerTest.andNot 60: [ OK ] SimdIntegerTest.andNot (0 ms) 60: [ RUN ] SimdIntegerTest.or 60: [ OK ] SimdIntegerTest.or (0 ms) 60: [ RUN ] SimdIntegerTest.xor 60: [ OK ] SimdIntegerTest.xor (0 ms) 60: [ RUN ] SimdIntegerTest.extract 60: [ OK ] SimdIntegerTest.extract (0 ms) 60: [ RUN ] SimdIntegerTest.cvtR2I 60: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvttR2I 60: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvtI2R 60: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpLt 60: [ OK ] SimdIntegerTest.cmpLt (0 ms) 60: [ RUN ] SimdIntegerTest.testBits 60: [ OK ] SimdIntegerTest.testBits (0 ms) 60: [ RUN ] SimdIntegerTest.andB 60: [ OK ] SimdIntegerTest.andB (0 ms) 60: [ RUN ] SimdIntegerTest.orB 60: [ OK ] SimdIntegerTest.orB (0 ms) 60: [ RUN ] SimdIntegerTest.anyTrue 60: [ OK ] SimdIntegerTest.anyTrue (0 ms) 60: [ RUN ] SimdIntegerTest.blend 60: [ OK ] SimdIntegerTest.blend (0 ms) 60: [ RUN ] SimdIntegerTest.cvtB2IB 60: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 60: [ RUN ] SimdIntegerTest.cvtIB2B 60: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 60: [----------] 23 tests from SimdIntegerTest (5 ms total) 60: 60: [----------] 56 tests from SimdMathTest 60: [ RUN ] SimdMathTest.generateTestPointsFloat 60: [ OK ] SimdMathTest.generateTestPointsFloat (1 ms) 60: [ RUN ] SimdMathTest.copysign 60: [ OK ] SimdMathTest.copysign (0 ms) 60: [ RUN ] SimdMathTest.invsqrt 60: [ OK ] SimdMathTest.invsqrt (4 ms) 60: [ RUN ] SimdMathTest.maskzInvsqrt 60: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPair 60: [ OK ] SimdMathTest.invsqrtPair (2 ms) 60: [ RUN ] SimdMathTest.sqrt 60: [ OK ] SimdMathTest.sqrt (0 ms) 60: [ RUN ] SimdMathTest.sqrtUnsafe 60: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 60: [ RUN ] SimdMathTest.inv 60: [ OK ] SimdMathTest.inv (0 ms) 60: [ RUN ] SimdMathTest.maskzInv 60: [ OK ] SimdMathTest.maskzInv (0 ms) 60: [ RUN ] SimdMathTest.cbrt 60: [ OK ] SimdMathTest.cbrt (0 ms) 60: [ RUN ] SimdMathTest.invcbrt 60: [ OK ] SimdMathTest.invcbrt (1 ms) 60: [ RUN ] SimdMathTest.log2 60: [ OK ] SimdMathTest.log2 (0 ms) 60: [ RUN ] SimdMathTest.log 60: [ OK ] SimdMathTest.log (0 ms) 60: [ RUN ] SimdMathTest.exp2 60: [ OK ] SimdMathTest.exp2 (1 ms) 60: [ RUN ] SimdMathTest.exp2Unsafe 60: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 60: [ RUN ] SimdMathTest.exp 60: [ OK ] SimdMathTest.exp (1 ms) 60: [ RUN ] SimdMathTest.expUnsafe 60: [ OK ] SimdMathTest.expUnsafe (0 ms) 60: [ RUN ] SimdMathTest.pow 60: [ OK ] SimdMathTest.pow (0 ms) 60: [ RUN ] SimdMathTest.powUnsafe 60: [ OK ] SimdMathTest.powUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erf 60: [ OK ] SimdMathTest.erf (0 ms) 60: [ RUN ] SimdMathTest.erfc 60: [ OK ] SimdMathTest.erfc (0 ms) 60: [ RUN ] SimdMathTest.sin 60: [ OK ] SimdMathTest.sin (0 ms) 60: [ RUN ] SimdMathTest.cos 60: [ OK ] SimdMathTest.cos (0 ms) 60: [ RUN ] SimdMathTest.tan 60: [ OK ] SimdMathTest.tan (1 ms) 60: [ RUN ] SimdMathTest.asin 60: [ OK ] SimdMathTest.asin (0 ms) 60: [ RUN ] SimdMathTest.acos 60: [ OK ] SimdMathTest.acos (0 ms) 60: [ RUN ] SimdMathTest.atan 60: [ OK ] SimdMathTest.atan (0 ms) 60: [ RUN ] SimdMathTest.atan2 60: [ OK ] SimdMathTest.atan2 (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrection 60: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrection 60: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracy 60: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.invSingleAccuracy 60: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.cbrtSingleAccuracy 60: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 60: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.log2SingleAccuracy 60: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.logSingleAccuracy 60: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracy 60: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 60: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracy 60: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracy 60: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erfSingleAccuracy 60: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.erfcSingleAccuracy 60: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sinSingleAccuracy 60: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.cosSingleAccuracy 60: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.tanSingleAccuracy 60: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.asinSingleAccuracy 60: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.acosSingleAccuracy 60: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atanSingleAccuracy 60: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atan2SingleAccuracy 60: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 56 tests from SimdMathTest (36 ms total) 60: 60: [----------] 1 test from EmptyArrayRefTest 60: [ RUN ] EmptyArrayRefTest.IsEmpty 60: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 60: [----------] 1 test from EmptyArrayRefTest (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/0.Assignment 60: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/1.Assignment 60: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/0.Basic 60: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/1.Basic 60: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 60: 60: [----------] 3 tests from SimdVectorOperationsTest 60: [ RUN ] SimdVectorOperationsTest.iprod 60: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 60: [ RUN ] SimdVectorOperationsTest.norm2 60: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 60: [ RUN ] SimdVectorOperationsTest.cprod 60: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 60: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 60: 60: [----------] 32 tests from Simd4FloatingpointTest 60: [ RUN ] Simd4FloatingpointTest.setZero 60: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 60: [ RUN ] Simd4FloatingpointTest.set 60: [ OK ] Simd4FloatingpointTest.set (0 ms) 60: [ RUN ] Simd4FloatingpointTest.add 60: [ OK ] Simd4FloatingpointTest.add (0 ms) 60: [ RUN ] Simd4FloatingpointTest.sub 60: [ OK ] Simd4FloatingpointTest.sub (0 ms) 60: [ RUN ] Simd4FloatingpointTest.mul 60: [ OK ] Simd4FloatingpointTest.mul (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fma 60: [ OK ] Simd4FloatingpointTest.fma (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fms 60: [ OK ] Simd4FloatingpointTest.fms (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fnma 60: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 60: [ RUN ] Simd4FloatingpointTest.fnms 60: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 60: [ RUN ] Simd4FloatingpointTest.abs 60: [ OK ] Simd4FloatingpointTest.abs (0 ms) 60: [ RUN ] Simd4FloatingpointTest.neg 60: [ OK ] Simd4FloatingpointTest.neg (0 ms) 60: [ RUN ] Simd4FloatingpointTest.and 60: [ OK ] Simd4FloatingpointTest.and (0 ms) 60: [ RUN ] Simd4FloatingpointTest.or 60: [ OK ] Simd4FloatingpointTest.or (0 ms) 60: [ RUN ] Simd4FloatingpointTest.xor 60: [ OK ] Simd4FloatingpointTest.xor (0 ms) 60: [ RUN ] Simd4FloatingpointTest.andNot 60: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 60: [ RUN ] Simd4FloatingpointTest.max 60: [ OK ] Simd4FloatingpointTest.max (0 ms) 60: [ RUN ] Simd4FloatingpointTest.min 60: [ OK ] Simd4FloatingpointTest.min (0 ms) 60: [ RUN ] Simd4FloatingpointTest.round 60: [ OK ] Simd4FloatingpointTest.round (0 ms) 60: [ RUN ] Simd4FloatingpointTest.trunc 60: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 60: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 60: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 60: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 60: [ RUN ] Simd4FloatingpointTest.selectByNotMask 60: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpNe 60: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpLe 60: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 60: [ RUN ] Simd4FloatingpointTest.cmpLt 60: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 60: [ RUN ] Simd4FloatingpointTest.andB 60: [ OK ] Simd4FloatingpointTest.andB (0 ms) 60: [ RUN ] Simd4FloatingpointTest.orB 60: [ OK ] Simd4FloatingpointTest.orB (0 ms) 60: [ RUN ] Simd4FloatingpointTest.anyTrue 60: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 60: [ RUN ] Simd4FloatingpointTest.blend 60: [ OK ] Simd4FloatingpointTest.blend (0 ms) 60: [ RUN ] Simd4FloatingpointTest.reduce 60: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 60: [ RUN ] Simd4FloatingpointTest.dotProduct 60: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 60: [ RUN ] Simd4FloatingpointTest.transpose 60: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 60: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 60: 60: [----------] 2 tests from Simd4MathTest 60: [ RUN ] Simd4MathTest.invsqrt 60: [ OK ] Simd4MathTest.invsqrt (0 ms) 60: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 60: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 60: [----------] 2 tests from Simd4MathTest (0 ms total) 60: 60: [----------] 1 test from Simd4VectorOperationsTest 60: [ RUN ] Simd4VectorOperationsTest.norm2 60: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 60: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 288 tests from 22 test suites ran. (52 ms total) 60: [ PASSED ] 288 tests. 60/104 Test #60: SimdUnitTests ............................. Passed 0.08 sec test 61 Start 61: CompatibilityHelpersTests 61: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/compat/tests 61: Test timeout computed to be: 60 61: [==========] Running 9 tests from 6 test suites. 61: [----------] Global test environment set-up. 61: [----------] 4 tests from TemplateMPTest 61: [ RUN ] TemplateMPTest.MpWithIndexInt 61: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexIntBad 61: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexBool 61: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexEnum 61: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 61: [----------] 4 tests from TemplateMPTest (0 ms total) 61: 61: [----------] 1 test from NotNullConstruction 61: [ RUN ] NotNullConstruction.Works 61: [ OK ] NotNullConstruction.Works (0 ms) 61: [----------] 1 test from NotNullConstruction (0 ms total) 61: 61: [----------] 1 test from NotNullCasting 61: [ RUN ] NotNullCasting.Works 61: [ OK ] NotNullCasting.Works (0 ms) 61: [----------] 1 test from NotNullCasting (0 ms total) 61: 61: [----------] 1 test from NotNullAssignment 61: [ RUN ] NotNullAssignment.Works 61: [ OK ] NotNullAssignment.Works (0 ms) 61: [----------] 1 test from NotNullAssignment (0 ms total) 61: 61: [----------] 1 test from MakeNotNull 61: [ RUN ] MakeNotNull.Works 61: [ OK ] MakeNotNull.Works (0 ms) 61: [----------] 1 test from MakeNotNull (0 ms total) 61: 61: [----------] 1 test from NotNull 61: [ RUN ] NotNull.WorksInContainers 61: [ OK ] NotNull.WorksInContainers (0 ms) 61: [----------] 1 test from NotNull (0 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 9 tests from 6 test suites ran. (0 ms total) 61: [ PASSED ] 9 tests. 61/104 Test #61: CompatibilityHelpersTests ................. Passed 0.02 sec test 62 Start 62: GmxAnaTest 62: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GmxAnaTest.xml" 62: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests 62: Test timeout computed to be: 600 62: [==========] Running 37 tests from 10 test suites. 62: [----------] Global test environment set-up. 62: [----------] 7 tests from Entropy 62: [ RUN ] Entropy.Schlitter_300_NoLinear 62: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 62: [ RUN ] Entropy.Schlitter_300_Linear 62: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_Linear 62: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 62: [ RUN ] Entropy.EntropyCompare_200_Linear 62: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 62: [ RUN ] Entropy.EntropyCompare_300_Linear 62: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 62: [----------] 7 tests from Entropy (4 ms total) 62: 62: [----------] 2 tests from GmxChiTest 62: [ RUN ] GmxChiTest.gmxchiWorksWithAll 62: Analyzing from residue 1 to residue 11 62: 10 residues with dihedrals found 62: 46 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 46 62: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithAll (464 ms) 62: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 62: Analyzing from residue 2 to residue 6 62: 5 residues with dihedrals found 62: 23 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 23 62: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (207 ms) 62: [----------] 2 tests from GmxChiTest (736 ms total) 62: 62: [----------] 10 tests from MindistTest 62: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistWorksWithSingleAtoms (10 ms) 62: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (1 ms) 62: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistDoesNotPickUpContacts (2 ms) 62: [ RUN ] MindistTest.mindistPicksUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 62: [ RUN ] MindistTest.ngWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.ngWorks (1 ms) 62: [ RUN ] MindistTest.groupWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.groupWorks (1 ms) 62: [ RUN ] MindistTest.maxDistWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.maxDistWorks (1 ms) 62: [ RUN ] MindistTest.noPbcWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.noPbcWorks (1 ms) 62: [ RUN ] MindistTest.resPerTimeWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.resPerTimeWorks (1 ms) 62: [ RUN ] MindistTest.matrixWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 5: 'atoms123' 62: Special case: making distance matrix between all atoms in group atoms123 62: [ OK ] MindistTest.matrixWorks (1 ms) 62: [----------] 10 tests from MindistTest (24 ms total) 62: 62: [----------] 1 test from GmxRmsTest 62: [ RUN ] GmxRmsTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Select group for least squares fit 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Select group for RMSD calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to -314880515 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 1: 'Protein' 62: Selected 1: 'Protein' 62: [ OK ] GmxRmsTest.BasicOutputWorks (157 ms) 62: [----------] 1 test from GmxRmsTest (157 ms total) 62: 62: [----------] 1 test from GmxRmsdistTest 62: [ RUN ] GmxRmsdistTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: 62: rmsmax = 0.382568, rmscmax = 0.659498 62: Setting the LD random seed to -186041533 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 0: 'System' 62: [ OK ] GmxRmsdistTest.BasicOutputWorks (155 ms) 62: [----------] 1 test from GmxRmsdistTest (156 ms total) 62: 62: [----------] 1 test from GmxRmsfTest 62: [ RUN ] GmxRmsfTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Select group(s) for root mean square calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to 2011609419 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 3: 'C-alpha' 62: [ OK ] GmxRmsfTest.BasicOutputWorks (153 ms) 62: [----------] 1 test from GmxRmsfTest (153 ms total) 62: 62: [----------] 1 test from GmxSorientTest 62: [ RUN ] GmxSorientTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Group 0 ( System) has 923 elements 62: Group 1 ( Protein) has 29 elements 62: Group 2 ( Protein-H) has 17 elements 62: Group 3 ( C-alpha) has 2 elements 62: Group 4 ( Backbone) has 6 elements 62: Group 5 ( MainChain) has 9 elements 62: Group 6 ( MainChain+Cb) has 11 elements 62: Group 7 ( MainChain+H) has 13 elements 62: Group 8 ( SideChain) has 16 elements 62: Group 9 ( SideChain-H) has 8 elements 62: Group 10 ( Prot-Masses) has 23 elements 62: Group 11 ( non-Protein) has 894 elements 62: Group 12 ( Water) has 894 elements 62: Group 13 ( SOL) has 894 elements 62: Group 14 ( non-Water) has 29 elements 62: Select a group: Select a group: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Average nr of molecules between 0 and 0.5 nm: 13.0 62: Average cos(theta1) between 0 and 0.5 nm: 0.103 62: Average 3cos2(theta2)-1 between 0 and 0.5 nm: -0.098 62: Setting the LD random seed to -286547970 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.pdb', all velocities are zero 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: Analysing residue names: 62: There are: 2 Protein residues 62: There are: 298 Water residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Select a group of reference particles and a solvent group: 62: Selected 1: 'Protein' 62: Selected 12: 'Water' 62: [ OK ] GmxSorientTest.BasicOutputWorks (111 ms) 62: [----------] 1 test from GmxSorientTest (111 ms total) 62: 62: [----------] 1 test from GmxRotmatTest 62: [ RUN ] GmxRotmatTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Setting the LD random seed to 2147483635 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 4: 'Backbone' 62: [ OK ] GmxRotmatTest.BasicOutputWorks (172 ms) 62: [----------] 1 test from GmxRotmatTest (172 ms total) 62: 62: [----------] 1 test from GmxSaltbrTest 62: [ RUN ] GmxSaltbrTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.tpr, VERSION 2026.3-Debian_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Setting the LD random seed to -2181389 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: This run will generate roughly 0 Mb of data 62: CG: SOL1-1 Q: -0.834 Atoms: 0 62: CG: SOL1-2 Q: 0.417 Atoms: 1 62: CG: SOL1-3 Q: 0.417 Atoms: 2 62: CG: SOL2-4 Q: -0.834 Atoms: 3 62: CG: SOL2-5 Q: 0.417 Atoms: 4 62: CG: SOL2-6 Q: 0.417 Atoms: 5 62: [ OK ] GmxSaltbrTest.BasicOutputWorks (5 ms) 62: [----------] 1 test from GmxSaltbrTest (5 ms total) 62: 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (2 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (2 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (2 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (3 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (2 ms) 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (28 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 37 tests from 10 test suites ran. (1549 ms total) 62: [ PASSED ] 37 tests. 62/104 Test #62: GmxAnaTest ................................ Passed 1.58 sec test 63 Start 63: GmxPreprocessTests 63: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests 63: Test timeout computed to be: 1920 63: [==========] Running 282 tests from 17 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertInteractionsTest 63: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 63: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 63: [----------] 1 test from ConvertInteractionsTest (0 ms total) 63: 63: [----------] 5 tests from GenconfTest 63: [ RUN ] GenconfTest.nbox_Works 63: [ OK ] GenconfTest.nbox_Works (4 ms) 63: [ RUN ] GenconfTest.nbox_norenumber_Works 63: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 63: [ RUN ] GenconfTest.nbox_dist_Works 63: [ OK ] GenconfTest.nbox_dist_Works (2 ms) 63: [ RUN ] GenconfTest.nbox_rot_Works 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 63: [ RUN ] GenconfTest.trj_Works 63: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 63: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Last frame 3 time 3.000 63: [ OK ] GenconfTest.trj_Works (2 ms) 63: [----------] 5 tests from GenconfTest (11 ms total) 63: 63: [----------] 2 tests from GenionTest 63: [ RUN ] GenionTest.HighConcentrationIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Group 0 ( System) has 653 elements 63: Group 1 ( Water) has 648 elements 63: Group 2 ( SOL) has 648 elements 63: Group 3 ( non-Water) has 5 elements 63: Group 4 ( Other) has 5 elements 63: Group 5 ( METH) has 5 elements 63: Select a group: Number of (3-atomic) solvent molecules: 216 63: Using random seed 1997. 63: Replacing solvent molecule 56 (atom 168) with NA 63: Replacing solvent molecule 120 (atom 360) with NA 63: Replacing solvent molecule 182 (atom 546) with NA 63: Replacing solvent molecule 71 (atom 213) with NA 63: Replacing solvent molecule 189 (atom 567) with CL 63: Replacing solvent molecule 54 (atom 162) with CL 63: Replacing solvent molecule 155 (atom 465) with CL 63: Replacing solvent molecule 99 (atom 297) with CL 63: 63: Setting the LD random seed to -1652560909 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: Will try to add 4 NA ions and 4 CL ions. 63: Select a continuous group of solvent molecules 63: Selected 1: 'Water' 63: [ OK ] GenionTest.HighConcentrationIonPlacement (200 ms) 63: [ RUN ] GenionTest.NoIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (single precision) 63: No ions to add, will just copy input configuration. 63: Setting the LD random seed to 1476093617 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GenionTest.NoIonPlacement (150 ms) 63: [----------] 2 tests from GenionTest (351 ms total) 63: 63: [----------] 1 test from GenRestrTest 63: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 63: 63: Reading structure file 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Select group to position restrain 63: Selected 3: 'C-alpha' 63: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 63: [----------] 1 test from GenRestrTest (1 ms total) 63: 63: [----------] 9 tests from PreprocessingAtomTypesTest 63: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 63: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 63: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 63: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 63: 63: [----------] 10 tests from PreprocessingBondAtomTypeTest 63: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 63: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 63: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 63: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 63: 63: [----------] 3 tests from GromppDirectiveTest 63: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to 2122308477 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -123478273 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (5 ms) 63: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 63: coefficients that do not sum to zero. This does not affect the simulation 63: and can be ignored, unless you are comparing potential energy values with 63: other force field ports and/or MD software. 63: First such dihedral in molecule A, involving atoms 0 2 1 3 63: 63: 63: NOTE 2 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -1351852049 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -19271190 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (2 ms) 63: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 63: Setting the LD random seed to 1492625819 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2137387951 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (13 ms) 63: [----------] 3 tests from GromppDirectiveTest (22 ms total) 63: 63: [----------] 6 tests from InsertMoleculesTest 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: 63: Added 1 molecules (out of 1 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 63: 63: Output configuration contains 8 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (4 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (4 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: Try 2 success (now 10 atoms)! 63: 63: Added 2 molecules (out of 2 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 63: 63: Output configuration contains 10 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (2 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 650 atoms)! 63: Try 2 success (now 652 atoms)! 63: Try 3 success (now 654 atoms)! 63: Try 4 success (now 656 atoms)! 63: 63: Added 4 molecules (out of 4 requested) 63: Replaced 8 residues (24 atoms) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 63: 63: Output configuration contains 632 atoms in 212 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (6 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Read 4 positions from file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 63: 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 63: Try 13 success (now 6 atoms)! 63: 63: Added 3 molecules (out of 4 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 63: 63: Output configuration contains 6 atoms in 3 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (3 ms) 63: [----------] 6 tests from InsertMoleculesTest (22 ms total) 63: 63: [----------] 3 tests from MassRepartitioning 63: [ RUN ] MassRepartitioning.ValidCaseWorks 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 63: [ RUN ] MassRepartitioning.UnboundGivesWarning 63: 63: WARNING 1 [file unknown]: 63: The are 1 atoms that have a mass below the mass repartitioning limit but 63: are not bound. These masses cannot be repartitioned. 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 63: [ RUN ] MassRepartitioning.LightPartnerGivesError 63: 63: ERROR 1 [file unknown]: 63: Light atoms are bound to at least one atom that has a too low mass for 63: repartitioning 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 63: [----------] 3 tests from MassRepartitioning (0 ms total) 63: 63: [----------] 36 tests from GetIrTest 63: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 63: Ignoring obsolete mdp entry 'title' 63: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (3 ms) 63: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 63: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (5 ms) 63: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) 63: [ RUN ] GetIrTest.RejectsValueWithoutKey 63: [ OK ] GetIrTest.RejectsValueWithoutKey (5 ms) 63: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 63: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (5 ms) 63: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (3 ms) 63: [ RUN ] GetIrTest.AcceptsEmptyLines 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 63: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstpcouple 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: With multiple time stepping, nstpcouple should be a multiple of 63: mts-factor 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: The Berendsen barostat does not generate any strictly correct ensemble, 63: and should not be used for new production simulations (in our opinion). 63: We recommend using the C-rescale barostat instead. 63: 63: 63: ERROR 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: compressibility must be > 0 when using pressure coupling Berendsen 63: 63: 63: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstdhdl 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstdhdl (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Lambda state must be set, either with init-lambda-state or with 63: init-lambda 63: 63: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 63: [ RUN ] GetIrTest.MtsCheckSDNotSupported 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: Multiple time stepping is only supported with integrator md 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 63: [ RUN ] GetIrTest.AcceptsElectricField 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 63: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 63: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (2 ms) 63: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsImplicitSolventNo (2 ms) 63: [ RUN ] GetIrTest.RejectsImplicitSolventYes 63: [ OK ] GetIrTest.RejectsImplicitSolventYes (4 ms) 63: [ RUN ] GetIrTest.AcceptsMimic 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsMimic (2 ms) 63: [ RUN ] GetIrTest.AcceptsTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 63: pull-coord2 has a non-zero force constant and is also referenced in 63: pull-coord1-expression. Make sure that this is intended. In most use 63: cases, the pull coordinates referenced by a transformation coordinate 63: should have their force constant set to zero. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 63: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (2 ms) 63: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 63: pull-coord2 can not use pull-coord1 in the transformation since this is a 63: constraint 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (2 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 63: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (2 ms) 63: [ RUN ] GetIrTest.MissingTransformationCoordExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 63: pull-coord1-expression not set for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (2 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 63: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 63: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 63: in total 100001 steps. This is not compatible with using soft-core 63: potentials. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (2 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 63: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.AcceptsFmmOptions 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsFmmOptions_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsFmmOptions (2 ms) 63: [----------] 36 tests from GetIrTest (96 ms total) 63: 63: [----------] 6 tests from SolvateTest 63: [ RUN ] SolvateTest.cs_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 1x1x1 boxes 63: Solvent box contains 270 atoms in 90 residues 63: Removed 129 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 47 residues 63: Generated solvent containing 141 atoms in 47 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 63: 63: Output configuration contains 141 atoms in 47 residues 63: Volume : 1.331 (nm^3) 63: Density : 1056.36 (g/l) 63: Number of solvent molecules: 47 63: 63: [ OK ] SolvateTest.cs_box_Works (3 ms) 63: [ RUN ] SolvateTest.cs_cp_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: [ OK ] SolvateTest.cs_cp_Works (12 ms) 63: [ RUN ] SolvateTest.cs_cp_p_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: Processing topology 63: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 63: [ OK ] SolvateTest.cs_cp_p_Works (13 ms) 63: [ RUN ] SolvateTest.shell_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 1902 solvent atoms more than 1.000000 nm from solute. 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 252 residues 63: Generated solvent containing 756 atoms in 252 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 63: 63: Output configuration contains 762 atoms in 254 residues 63: Volume : 27.2709 (nm^3) 63: Density : 279.3 (g/l) 63: Number of solvent molecules: 252 63: 63: [ OK ] SolvateTest.shell_Works (7 ms) 63: [ RUN ] SolvateTest.update_Topology_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 3x3x3 boxes 63: Solvent box contains 14952 atoms in 4984 residues 63: Removed 2787 solvent atoms due to solvent-solvent overlap 63: Removed 30 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 2 different molecule types: 63: HOH ( 3 atoms): 1876 residues 63: SOL ( 3 atoms): 2169 residues 63: Generated solvent containing 0 atoms in 0 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 63: 63: Output configuration contains 12141 atoms in 4047 residues 63: Volume : 125 (nm^3) 63: Density : 968.963 (g/l) 63: Number of solvent molecules: 4045 63: 63: Processing topology 63: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: [ OK ] SolvateTest.update_Topology_Works (48 ms) 63: [ RUN ] SolvateTest.cs_pdb_big_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 1218 atoms in 406 residues 63: Removed 555 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 221 residues 63: Generated solvent containing 663 atoms in 221 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 63: 63: Output configuration contains 663 atoms in 221 residues 63: Volume : 8 (nm^3) 63: Density : 826.409 (g/l) 63: Number of solvent molecules: 221 63: 63: [ OK ] SolvateTest.cs_pdb_big_box_Works (5 ms) 63: [----------] 6 tests from SolvateTest (91 ms total) 63: 63: [----------] 1 test from TopDirTests 63: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 63: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 63: [----------] 1 test from TopDirTests (0 ms total) 63: 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (2 ms total) 63: 63: [----------] 45 tests from SinglePeptideFragments/EditconfTest 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (4 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (3 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 63: 63: Select a group for output: 63: Group 0 ( two_residues) has 23 elements 63: There is one group in the index 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (3 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : 0.212 1.187 3.527 (nm) 63: new center : 4.028 2.819 3.723 (nm) 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.42 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.42 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.42 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: shift : -0.814 1.104 2.657 (nm) 63: new center : 3.002 2.736 2.852 (nm) 63: new box vectors : 6.004 5.472 5.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 187.40 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (3 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.28 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (3 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.28 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.28 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (3 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (3 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (2 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) 63: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 63: Note that major changes are planned in future for editconf, to improve usability and utility. 63: Read 252 atoms 63: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 63: No velocities found 63: system size : 2.004 1.472 1.704 (nm) 63: center : 3.816 1.632 0.195 (nm) 63: box vectors : 8.056 5.637 7.445 (nm) 63: box angles : 90.00 90.00 90.00 (degrees) 63: box volume : 338.10 (nm^3) 63: new center : 3.816 1.632 0.195 (nm) 63: new box vectors : 5.004 4.472 4.704 (nm) 63: new box angles : 90.00 90.00 90.00 (degrees) 63: new box volume : 105.27 (nm^3) 63: 63: WARNING: No boxtype specified - distance condition applied in each dimension. 63: If the molecule rotates the actual distance will be smaller. You might want 63: to use a cubic box instead, or why not try a dodecahedron today? 63: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (2 ms) 63: [----------] 45 tests from SinglePeptideFragments/EditconfTest (113 ms total) 63: 63: [----------] 16 tests from CorrectVelocity/MaxwellTest 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (1 ms) 63: [----------] 16 tests from CorrectVelocity/MaxwellTest (20 ms total) 63: 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -546859521 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -369383971 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -536877575 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -271974405 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -17608929 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1076118193 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -546836579 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -840009227 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -1145667729 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -5309570 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to 2145501179 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -346431523 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -536877129 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -454992145 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -327202353 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1056628719 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -541197643 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to 1471151007 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 (5 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -146117674 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -437291217 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to 1739451809 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -604303745 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to 2134832991 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -471126529 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -46148321 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to 1589363550 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -293603489 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -882393089 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to 2080373662 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to 197100921 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -67420163 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -306512422 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -543432721 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1644310546 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 (2 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -303579145 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -8523907 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.tpr, VERSION 2026.3-Debian_1 (single precision) 63: Setting the LD random seed to -7244309 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1082812517 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 (3 ms) 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest (81 ms total) 63: 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 63: Setting the LD random seed to 2146401519 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (16 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 63: Setting the LD random seed to -957527109 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (10 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -1212285001 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1341707316 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (5 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -820529159 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1138884609 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to 922609399 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -897886465 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to 1475869887 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1476405785 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (4 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 63: Setting the LD random seed to 1543503807 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (12 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 63: Setting the LD random seed to -10780929 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -809588994 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (17 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 63: Setting the LD random seed to -949489937 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (11 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 63: Setting the LD random seed to -1083724993 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -316702755 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (12 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 63: Setting the LD random seed to -546050310 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1658256095 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (12 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 63: Setting the LD random seed to -1213333799 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 872411111 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (13 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 63: Setting the LD random seed to -194290177 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -809633809 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (12 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 63: Setting the LD random seed to -584139929 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -637538318 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (12 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 63: Setting the LD random seed to -114630766 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1970241469 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (7 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 63: Setting the LD random seed to 2146426814 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -598122753 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (7 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -1158161665 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -539239298 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (6 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to 1459607789 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -34164741 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (9 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 63: Setting the LD random seed to -1092618497 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (17 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 63: Setting the LD random seed to -3224169 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1074538631 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (14 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 63: Setting the LD random seed to -1880571921 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (11 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -649134885 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1293467661 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (6 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 63: Setting the LD random seed to -555753124 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (14 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 63: Setting the LD random seed to -1070072833 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1644162478 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 (11 ms) 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest (260 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 282 tests from 17 test suites ran. (1075 ms total) 63: [ PASSED ] 242 tests. 63: [ SKIPPED ] 40 tests, listed below: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63/104 Test #63: GmxPreprocessTests ........................ Passed 1.10 sec test 64 Start 64: Pdb2gmx1Test 64: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 64: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests 64: Test timeout computed to be: 1920 64: [==========] Running 30 tests from 1 test suite. 64: [----------] Global test environment set-up. 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (50 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (52 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (52 ms) 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest (780 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 30 tests from 1 test suite ran. (780 ms total) 64: [ PASSED ] 30 tests. 64/104 Test #64: Pdb2gmx1Test .............................. Passed 0.79 sec test 65 Start 65: Pdb2gmx2Test 65: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 65: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests 65: Test timeout computed to be: 1920 65: [==========] Running 40 tests from 2 test suites. 65: [----------] Global test environment set-up. 65: [----------] 20 tests from G43a1/Pdb2gmxTest 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (45 ms) 65: [----------] 20 tests from G43a1/Pdb2gmxTest (561 ms total) 65: 65: [----------] 20 tests from G53a6/Pdb2gmxTest 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (28 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (28 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (52 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (59 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (57 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (33 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (48 ms) 65: [----------] 20 tests from G53a6/Pdb2gmxTest (708 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 40 tests from 2 test suites ran. (1270 ms total) 65: [ PASSED ] 40 tests. 65/104 Test #65: Pdb2gmx2Test .............................. Passed 1.29 sec test 66 Start 66: Pdb2gmx3Test 66: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 66: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/gmxpreprocess/tests 66: Test timeout computed to be: 1920 66: [==========] Running 55 tests from 9 test suites. 66: [----------] Global test environment set-up. 66: [----------] 10 tests from Amber/Pdb2gmxTest 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (33 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (28 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (62 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (29 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (30 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (28 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (128 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (162 ms) 66: [----------] 10 tests from Amber/Pdb2gmxTest (555 ms total) 66: 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest 66: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber99sb-ildn force field and the tip4p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (20 ms) 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest (20 ms total) 66: 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (54 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (30 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest (329 ms total) 66: 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the opc water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (11 ms) 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the tip4pew water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (9 ms) 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest (21 ms total) 66: 66: [----------] 12 tests from Charmm/Pdb2gmxTest 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (30 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 0 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (13 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (57 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 8 virtual sites 66: Added 2 dummy masses 66: Added 3 new constraints 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 9 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (12 ms) 66: [----------] 12 tests from Charmm/Pdb2gmxTest (347 ms total) 66: 66: [----------] 8 tests from ChainSep/Pdb2gmxTest 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (24 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 7 acceptors were found. 66: There are 7 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS8 66: NE223 66: MET12 SD55 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 317 pairs 66: Before cleaning: 322 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 7 58 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (58 atoms, 7 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 124 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 125, now 125 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 5 cmap torsion pairs 66: 66: There are 322 dihedrals, 19 impropers, 227 angles 66: 314 pairs, 125 bonds and 0 virtual sites 66: 66: Total mass 846.083 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 124 atoms 7 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (22 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (23 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 12 acceptors were found. 66: There are 13 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 66: SG9 66: HIS8 NE251 1.055 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 288 pairs 66: Before cleaning: 293 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 8 61 66: 66: 2 'B' 3 25 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (61 atoms, 8 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 8 residues with 114 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 115, now 115 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6 cmap torsion pairs 66: 66: There are 293 dihedrals, 23 impropers, 203 angles 66: 285 pairs, 115 bonds and 0 virtual sites 66: 66: Total mass 888.952 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 114 atoms 8 residues 66: 66: Including chain 2 in system: 61 atoms 3 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (23 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 650 pairs 66: Before cleaning: 660 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 3 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 261 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 260, now 260 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 8 cmap torsion pairs 66: 66: There are 660 dihedrals, 45 impropers, 466 angles 66: 647 pairs, 260 bonds and 0 virtual sites 66: 66: Total mass 1900.162 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (23 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 6 donors and 4 acceptors were found. 66: There are 3 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 164 pairs 66: Before cleaning: 169 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 4 33 66: 66: 3 'B' 3 25 66: 66: 4 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (33 atoms, 4 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 66 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 67, now 67 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 169 dihedrals, 13 impropers, 118 angles 66: 161 pairs, 67 bonds and 0 virtual sites 66: 66: Total mass 472.547 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 4 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 66 atoms 4 residues 66: 66: Including chain 3 in system: 61 atoms 3 residues 66: 66: Including chain 4 in system: 83 atoms 5 residues 66: 66: Now there are 261 atoms and 16 residues 66: 66: Total mass in system 1900.162 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (24 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 652 pairs 66: Before cleaning: 662 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 256, now 256 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 12 cmap torsion pairs 66: 66: There are 662 dihedrals, 47 impropers, 460 angles 66: 649 pairs, 256 bonds and 0 virtual sites 66: 66: Total mass 1864.131 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (22 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 14 donors and 15 acceptors were found. 66: There are 20 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 441 pairs 66: Before cleaning: 446 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 11 86 66: 66: 2 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (86 atoms, 11 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 11 residues with 172 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 173, now 173 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 9 cmap torsion pairs 66: 66: There are 446 dihedrals, 29 impropers, 312 angles 66: 438 pairs, 173 bonds and 0 virtual sites 66: 66: Total mass 1262.488 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 172 atoms 11 residues 66: 66: Including chain 2 in system: 83 atoms 5 residues 66: 66: Now there are 255 atoms and 16 residues 66: 66: Total mass in system 1864.131 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (21 ms) 66: [----------] 8 tests from ChainSep/Pdb2gmxTest (189 ms total) 66: 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (15 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (14 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (15 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge -0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (15 ms) 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest (62 ms total) 66: 66: [----------] 4 tests from Cyclic/Pdb2gmxTest 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: Moved all the water blocks to the end 66: 66: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 71 1527 66: 66: 2 'Q' 71 1527 66: 66: 3 'Q' 7 7 66: 66: 4 ' ' 10 10 (only water) 66: 66: 5 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'Q' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'Q' (7 atoms, 7 residues) 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 7 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: No bonds 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 0 angles 66: 0 pairs, 0 bonds and 0 virtual sites 66: 66: Total mass 170.135 a.m.u. 66: 66: Total charge 14.000 e 66: 66: Writing topology 66: 66: Processing chain 4 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 5 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain m9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: olecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 2297 atoms 71 residues 66: 66: Including chain 2 in system: 2297 atoms 71 residues 66: 66: Including chain 3 in system: 7 atoms 7 residues 66: 66: Including chain 4 in system: 30 atoms 10 residues 66: 66: Including chain 5 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.562 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (348 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (180 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 12080 pairs 66: Before cleaning: 13210 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Moved all the water blocks to the end 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 149 3061 66: 66: 2 ' ' 10 10 (only water) 66: 66: 3 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (3061 atoms, 149 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 149 residues with 4601 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4962, now 4962 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 13210 dihedrals, 366 impropers, 8868 angles 66: 11654 pairs, 4962 bonds and 0 virtual sites 66: 66: Total mass 46139.162 a.m.u. 66: 66: Total charge -128.000 e 66: 66: Writing topology 66: 66: Processing chain 2 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 3 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 4601 atoms 149 residues 66: 66: Including chain 2 in system: 30 atoms 10 residues 66: 66: Including chain 3 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.562 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (362 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (55 ms) 66: [----------] 4 tests from Cyclic/Pdb2gmxTest (948 ms total) 66: 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 5 47 66: 66: 2 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2325 dihedrals, 141 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.100 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 86 atoms 5 residues 66: 66: Including chain 2 in system: 878 atoms 60 residues 66: 66: Now there are 964 atoms and 65 residues 66: 66: Total mass in system 6519.802 a.m.u. 66: 66: Total charge in system 4.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file (70 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 188 pairs 66: Before cleaning: 198 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 3 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 4 38 66: 66: 2 'E' 5 47 66: 66: 3 'F' 5 47 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (38 atoms, 4 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 72 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 75, now 74 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 198 dihedrals, 18 impropers, 132 angles 66: 185 pairs, 74 bonds and 0 virtual sites 66: 66: Total mass 543.584 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'E' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'F' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 72 atoms 4 residues 66: 66: Including chain 2 in system: 86 atoms 5 residues 66: 66: Including chain 3 in system: 86 atoms 5 residues 66: 66: Now there are 244 atoms and 14 residues 66: 66: Total mass in system 1850.988 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file (29 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 2558 pairs 66: Before cleaning: 2568 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 65 460 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (460 atoms, 65 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 65 residues with 964 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 969, now 969 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2568 dihedrals, 164 impropers, 1773 angles 66: 2549 pairs, 969 bonds and 0 virtual sites 66: 66: Total mass 6519.802 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file (57 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 654 pairs 66: Before cleaning: 684 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 14 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (132 atoms, 14 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 14 residues with 244 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 253, now 252 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 684 dihedrals, 64 impropers, 450 angles 66: 645 pairs, 252 bonds and 0 virtual sites 66: 66: Total mass 1850.988 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file (24 ms) 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest (183 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 55 tests from 9 test suites ran. (2660 ms total) 66: [ PASSED ] 55 tests. 66/104 Test #66: Pdb2gmx3Test .............................. Passed 2.67 sec test 67 Start 67: CorrelationsTest 67: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/CorrelationsTest.xml" 67: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/correlationfunctions/tests 67: Test timeout computed to be: 60 67: [==========] Running 21 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 10 tests from AutocorrTest 67: [ RUN ] AutocorrTest.EacNormal 67: [ OK ] AutocorrTest.EacNormal (14 ms) 67: [ RUN ] AutocorrTest.EacNoNormalize 67: [ OK ] AutocorrTest.EacNoNormalize (10 ms) 67: [ RUN ] AutocorrTest.EacCos 67: [ OK ] AutocorrTest.EacCos (18 ms) 67: [ RUN ] AutocorrTest.EacVector 67: [ OK ] AutocorrTest.EacVector (34 ms) 67: [ RUN ] AutocorrTest.EacRcross 67: [ OK ] AutocorrTest.EacRcross (2 ms) 67: [ RUN ] AutocorrTest.EacP0 67: [ OK ] AutocorrTest.EacP0 (34 ms) 67: [ RUN ] AutocorrTest.EacP1 67: [ OK ] AutocorrTest.EacP1 (31 ms) 67: [ RUN ] AutocorrTest.EacP2 67: [ OK ] AutocorrTest.EacP2 (65 ms) 67: [ RUN ] AutocorrTest.EacP3 67: [ OK ] AutocorrTest.EacP3 (4 ms) 67: [ RUN ] AutocorrTest.EacP4 67: [ OK ] AutocorrTest.EacP4 (35 ms) 67: [----------] 10 tests from AutocorrTest (255 ms total) 67: 67: [----------] 10 tests from ExpfitTest 67: [ RUN ] ExpfitTest.EffnEXP1 67: [ OK ] ExpfitTest.EffnEXP1 (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP2 67: [ OK ] ExpfitTest.EffnEXP2 (1 ms) 67: [ RUN ] ExpfitTest.EffnEXPEXP 67: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP5 67: [ OK ] ExpfitTest.EffnEXP5 (4 ms) 67: [ RUN ] ExpfitTest.EffnEXP7 67: [ OK ] ExpfitTest.EffnEXP7 (3 ms) 67: [ RUN ] ExpfitTest.EffnEXP9 67: [ OK ] ExpfitTest.EffnEXP9 (14 ms) 67: [ RUN ] ExpfitTest.EffnERF 67: [ OK ] ExpfitTest.EffnERF (2 ms) 67: [ RUN ] ExpfitTest.EffnERREST 67: [ OK ] ExpfitTest.EffnERREST (2 ms) 67: [ RUN ] ExpfitTest.EffnVAC 67: [ OK ] ExpfitTest.EffnVAC (5 ms) 67: [ RUN ] ExpfitTest.EffnPRES 67: [ OK ] ExpfitTest.EffnPRES (10 ms) 67: [----------] 10 tests from ExpfitTest (49 ms total) 67: 67: [----------] 1 test from ManyAutocorrelationTest 67: [ RUN ] ManyAutocorrelationTest.Empty 67: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 67: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 21 tests from 3 test suites ran. (312 ms total) 67: [ PASSED ] 21 tests. 67/104 Test #67: CorrelationsTest .......................... Passed 0.33 sec test 68 Start 68: AnalysisDataUnitTests 68: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/analysisdata/tests 68: Test timeout computed to be: 60 68: [==========] Running 69 tests from 14 test suites. 68: [----------] Global test environment set-up. 68: [----------] 3 tests from AnalysisDataInitializationTest 68: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 68: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 68: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/1 (3 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/2 (4 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/3 (3 ms total) 68: 68: [----------] 4 tests from AnalysisArrayDataTest 68: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 68: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisArrayDataTest.StorageWorks 68: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 68: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 68: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 68: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 68: 68: [----------] 6 tests from AverageModuleTest 68: [ RUN ] AverageModuleTest.BasicTest 68: [ OK ] AverageModuleTest.BasicTest (1 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipointData 68: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 68: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 68: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 68: [ OK ] AverageModuleTest.HandlesDataSetAveraging (1 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeXAxis 68: [ OK ] AverageModuleTest.CanCustomizeXAxis (1 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 68: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 68: [----------] 6 tests from AverageModuleTest (9 ms total) 68: 68: [----------] 2 tests from FrameAverageModuleTest 68: [ RUN ] FrameAverageModuleTest.BasicTest 68: [ OK ] FrameAverageModuleTest.BasicTest (1 ms) 68: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 68: [----------] 2 tests from FrameAverageModuleTest (2 ms total) 68: 68: [----------] 7 tests from AnalysisHistogramSettingsTest 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 68: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 68: 68: [----------] 2 tests from SimpleHistogramModuleTest 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (2 ms) 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 68: [----------] 2 tests from SimpleHistogramModuleTest (4 ms total) 68: 68: [----------] 3 tests from WeightedHistogramModuleTest 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 68: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 68: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 68: [----------] 3 tests from WeightedHistogramModuleTest (5 ms total) 68: 68: [----------] 3 tests from BinAverageModuleTest 68: [ RUN ] BinAverageModuleTest.ComputesCorrectly 68: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 68: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 68: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 68: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 68: [----------] 3 tests from BinAverageModuleTest (4 ms total) 68: 68: [----------] 4 tests from AbstractAverageHistogramTest 68: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 68: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 68: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (2 ms) 68: [----------] 4 tests from AbstractAverageHistogramTest (5 ms total) 68: 68: [----------] 3 tests from LifetimeModuleTest 68: [ RUN ] LifetimeModuleTest.BasicTest 68: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 68: [ RUN ] LifetimeModuleTest.CumulativeTest 68: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 68: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 68: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 68: [----------] 3 tests from LifetimeModuleTest (3 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 69 tests from 14 test suites ran. (53 ms total) 68: [ PASSED ] 69 tests. 68/104 Test #68: AnalysisDataUnitTests ..................... Passed 0.08 sec test 69 Start 69: CoordinateIOTests 69: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/CoordinateIOTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/coordinateio/tests 69: Test timeout computed to be: 60 69: [==========] Running 67 tests from 20 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from OutputSelectorDeathTest 69: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (5 ms) 69: [----------] 1 test from OutputSelectorDeathTest (5 ms total) 69: 69: [----------] 5 tests from TrajectoryFrameWriterTest 69: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (4 ms) 69: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 69: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 69: [----------] 5 tests from TrajectoryFrameWriterTest (10 ms total) 69: 69: [----------] 5 tests from OutputAdapterContainer 69: [ RUN ] OutputAdapterContainer.MakeEmpty 69: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 69: [ RUN ] OutputAdapterContainer.AddAdapter 69: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectBadAdapter 69: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 69: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 69: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 69: [----------] 5 tests from OutputAdapterContainer (0 ms total) 69: 69: [----------] 3 tests from RegisterFrameConverterTest 69: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 69: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 69: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 69: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 69: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 69: 69: [----------] 5 tests from FlagTest 69: [ RUN ] FlagTest.CanSetSimpleFlag 69: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 69: [ RUN ] FlagTest.CanAddNewBox 69: [ OK ] FlagTest.CanAddNewBox (0 ms) 69: [ RUN ] FlagTest.SetsImplicitPrecisionChange 69: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitStartTimeChange 69: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitTimeStepChange 69: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 69: [----------] 5 tests from FlagTest (0 ms total) 69: 69: [----------] 5 tests from SetAtomsTest 69: [ RUN ] SetAtomsTest.RemovesExistingAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.RemovesExistingAtoms (2 ms) 69: [ RUN ] SetAtomsTest.AddsNewAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) 69: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (2 ms) 69: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (1 ms) 69: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (3 ms) 69: [----------] 5 tests from SetAtomsTest (12 ms total) 69: 69: [----------] 2 tests from SetBothTimeTest 69: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 69: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 69: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 69: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 69: [----------] 2 tests from SetBothTimeTest (0 ms total) 69: 69: [----------] 2 tests from SetStartTimeTest 69: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 69: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 69: [ RUN ] SetStartTimeTest.WorksWithZeroStart 69: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 69: [----------] 2 tests from SetStartTimeTest (0 ms total) 69: 69: [----------] 1 test from SetTimeStepTest 69: [ RUN ] SetTimeStepTest.SetTimeStepWorks 69: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 69: [----------] 1 test from SetTimeStepTest (0 ms total) 69: 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (2 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (2 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (13 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (2 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (2 ms) 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (6 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (3 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (3 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (4 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (14 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (1 ms) 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (5 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (2 ms) 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (4 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput (5 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 67 tests from 20 test suites ran. (83 ms total) 69: [ PASSED ] 67 tests. 69/104 Test #69: CoordinateIOTests ......................... Passed 0.11 sec test 70 Start 70: TrajectoryAnalysisUnitTests 70: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests 70: Test timeout computed to be: 1920 70: [==========] Running 394 tests from 21 test suites. 70: [----------] Global test environment set-up. 70: [----------] 11 tests from AngleModuleTest 70: [ RUN ] AngleModuleTest.ComputesSimpleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesSimpleAngles (4 ms) 70: [ RUN ] AngleModuleTest.ComputesDihedrals 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesDihedrals (2 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPairAngles (3 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (2 ms) 70: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (2 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (2 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system for different angles', 33 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (2 ms) 70: [ RUN ] AngleModuleTest.ComputesMultipleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesMultipleAngles (3 ms) 70: [ RUN ] AngleModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesDynamicSelections (2 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (2 ms) 70: [----------] 11 tests from AngleModuleTest (31 ms total) 70: 70: [----------] 5 tests from ClustsizeTest 70: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 2, cmax: 4, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (3 ms) 70: [ RUN ] ClustsizeTest.NoMolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 1, cmax: 6, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (3 ms) 70: [ RUN ] ClustsizeTest.MolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (3 ms) 70: [ RUN ] ClustsizeTest.MolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 1, cmax: 6, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (3 ms) 70: [ RUN ] ClustsizeTest.MolCSize 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolCSize (3 ms) 70: [----------] 5 tests from ClustsizeTest (18 ms total) 70: 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (2 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (5 ms total) 70: 70: [----------] 4 tests from ConvertTrjModuleTest 70: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (8 ms) 70: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 70: [----------] 4 tests from ConvertTrjModuleTest (17 ms total) 70: 70: [----------] 6 tests from DistanceModuleTest 70: [ RUN ] DistanceModuleTest.ComputesDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: [ OK ] DistanceModuleTest.ComputesDistances (2 ms) 70: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 70: Number of samples: 4 70: Average distance: 1.81066 nm 70: Standard deviation: 0.79289 nm 70: [ OK ] DistanceModuleTest.ComputesMultipleDistances (2 ms) 70: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2 and res_cog x < 2.8: 70: Number of samples: 3 70: Average distance: 1.72076 nm 70: Standard deviation: 1.24839 nm 70: [ OK ] DistanceModuleTest.HandlesDynamicSelections (2 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: Contacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (6 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: SuccessiveContacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (5 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: ManyContacts: 70: Number of samples: 10 70: Average distance: 1.82913 nm 70: Standard deviation: 0.78478 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (5 ms) 70: [----------] 6 tests from DistanceModuleTest (27 ms total) 70: 70: [----------] 2 tests from ExtractClusterModuleTest 70: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 70: trr version: GMX_trn_file (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (4 ms) 70: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 70: [----------] 2 tests from ExtractClusterModuleTest (5 ms total) 70: 70: [----------] 2 tests from FreeVolumeModuleTest 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for 40 particles. These were set to zero. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 13 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.02 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 70: Fractional free volume 0.194 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (41 ms) 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 17 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.48 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 70: Fractional free volume 0.200 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (40 ms) 70: [----------] 2 tests from FreeVolumeModuleTest (82 ms total) 70: 70: [----------] 13 tests from MsdModuleTest 70: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.threeDimensionalDiffusion (3 ms) 70: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.twoDimensionalDiffusion (2 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusion (2 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (3 ms) 70: [ RUN ] MsdModuleTest.multipleGroupsWork 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to 972978671 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.multipleGroupsWork (17 ms) 70: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.100 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 70: Analyzed 21 frames, last time 2.000 70: Setting the LD random seed to -67436690 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (17 ms) 70: [ RUN ] MsdModuleTest.trestartLessThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1382023185 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartLessThanDt (13 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -92291639 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDt (17 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -965380642 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (12 ms) 70: [ RUN ] MsdModuleTest.molTest 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -152568965 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.molTest (16 ms) 70: [ RUN ] MsdModuleTest.beginFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to 2147180524 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.beginFit (16 ms) 70: [ RUN ] MsdModuleTest.endFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -1174936844 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.endFit (16 ms) 70: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: NOTE: You provided an index file 70: /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 70: (with -n), but it was not used by any selection. 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -1343793433 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (15 ms) 70: [----------] 13 tests from MsdModuleTest (160 ms total) 70: 70: [----------] 9 tests from PairDistanceModuleTest 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistances (2 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (3 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (2 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (2 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (2 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (2 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (2 ms) 70: [----------] 9 tests from PairDistanceModuleTest (24 ms total) 70: 70: [----------] 5 tests from RdfModuleTest 70: [ RUN ] RdfModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.BasicTest (12 ms) 70: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 70: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (9 ms) 70: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (11 ms) 70: [ RUN ] RdfModuleTest.CalculatesSurf 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesSurf (6 ms) 70: [ RUN ] RdfModuleTest.CalculatesXY 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesXY (12 ms) 70: [----------] 5 tests from RdfModuleTest (53 ms total) 70: 70: [----------] 5 tests from SasaModuleTest 70: [ RUN ] SasaModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.BasicTest (8 ms) 70: [ RUN ] SasaModuleTest.HandlesSelectedResidues 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesSelectedResidues (4 ms) 70: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (4 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (6 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (7 ms) 70: [----------] 5 tests from SasaModuleTest (33 ms total) 70: 70: [----------] 9 tests from SelectModuleTest 70: [ RUN ] SelectModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.BasicTest (4 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (4 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (2 ms) 70: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (3 ms) 70: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (3 ms) 70: [ RUN ] SelectModuleTest.NormalizesSizes 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 70: [ RUN ] SelectModuleTest.WritesResidueNumbers 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueNumbers (2 ms) 70: [ RUN ] SelectModuleTest.WritesResidueIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueIndices (2 ms) 70: [ RUN ] SelectModuleTest.HandlesPrimeInAtomName 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.HandlesPrimeInAtomName (2 ms) 70: [----------] 9 tests from SelectModuleTest (29 ms total) 70: 70: [----------] 10 tests from SurfaceAreaTest 70: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 70: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 70: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 70: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints12 70: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints32 70: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints42 70: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints122 70: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 70: [ RUN ] SurfaceAreaTest.Computes100Points 70: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (3 ms) 70: [----------] 10 tests from SurfaceAreaTest (11 ms total) 70: 70: [----------] 4 tests from TopologyInformation 70: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 70: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 70: [ RUN ] TopologyInformation.WorksWithGroFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 70: [ RUN ] TopologyInformation.WorksWithPdbFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 70: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file lysozyme.top, line 1465]: 70: System has non-zero total charge: 2.000000 70: Total charge should normally be an integer. See 70: https://manual.gromacs.org/current/user-guide/floating-point.html 70: for discussion on how close it should be to an integer. 70: 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 465.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 70: Setting the LD random seed to -268720193 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 70: Analysing residue names: 70: There are: 10 Protein residues 70: Analysing Protein... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (214 ms) 70: [----------] 4 tests from TopologyInformation (217 ms total) 70: 70: [----------] 4 tests from TrajectoryModuleTest 70: [ RUN ] TrajectoryModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.BasicTest (2 ms) 70: [ RUN ] TrajectoryModuleTest.PlotsXOnly 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.PlotsXOnly (3 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (2 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoForces 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoForces (3 ms) 70: [----------] 4 tests from TrajectoryModuleTest (12 ms total) 70: 70: [----------] 5 tests from UnionFinderTest 70: [ RUN ] UnionFinderTest.WorksEmpty 70: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 70: [ RUN ] UnionFinderTest.BasicMerges 70: [ OK ] UnionFinderTest.BasicMerges (0 ms) 70: [ RUN ] UnionFinderTest.LargerMerges 70: [ OK ] UnionFinderTest.LargerMerges (0 ms) 70: [ RUN ] UnionFinderTest.LongRightMerge 70: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 70: [ RUN ] UnionFinderTest.LongLeftMerge 70: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 70: [----------] 5 tests from UnionFinderTest (0 ms total) 70: 70: [----------] 1 test from MappedUnionFinderTest 70: [ RUN ] MappedUnionFinderTest.BasicMerges 70: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 70: [----------] 1 test from MappedUnionFinderTest (0 ms total) 70: 70: [----------] 192 tests from MoleculeTests/DsspModuleTest 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (18 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (8 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (9 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (10 ms) 70: [----------] 192 tests from MoleculeTests/DsspModuleTest (2313 ms total) 70: 70: [----------] 3 tests from GyrateTests/GyrateModuleTest 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (7 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (5 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (6 ms) 70: [----------] 3 tests from GyrateTests/GyrateModuleTest (18 ms total) 70: 70: [----------] 96 tests from HBondTests/HbondModuleTest 70: [ RUN ] HBondTests/HbondModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/0 (10 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/1 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/2 (10 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/3 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/3 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/4 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/4 (10 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/5 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/5 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/6 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/6 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/7 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/7 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/8 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/8 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/9 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/9 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/10 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/10 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/11 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/11 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/12 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/12 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/13 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/13 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/14 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/14 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/15 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/15 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/16 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/16 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/17 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/17 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/18 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/18 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/19 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/19 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/20 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/20 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/21 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/21 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/22 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/22 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/23 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/23 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/24 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/24 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/25 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/25 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/26 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/26 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/27 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/27 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/28 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/28 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/29 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/29 (9 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/30 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/30 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/31 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/31 (8 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/32 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/32 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/33 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/33 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/34 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/34 (47 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/35 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/35 (77 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/36 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/36 (52 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/37 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/37 (51 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/38 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/38 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/39 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/39 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/40 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/40 (64 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/41 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/41 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/42 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/42 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/43 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/43 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/44 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/44 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/45 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/45 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/46 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/46 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/47 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/47 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/48 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/48 (73 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/49 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/49 (55 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/50 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/50 (62 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/51 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/51 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/52 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/52 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/53 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/53 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/54 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/54 (47 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/55 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/55 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/56 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/56 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/57 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/57 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/58 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/58 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/59 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/59 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/60 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/60 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/61 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/61 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/62 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/62 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/63 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/63 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/64 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/64 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/65 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/65 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/66 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/66 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/67 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/67 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/68 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/68 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/69 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/69 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/70 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/70 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/71 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/71 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/72 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/72 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/73 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/73 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/74 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/74 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/75 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/75 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/76 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/76 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/77 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/77 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/78 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/78 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/79 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/79 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/80 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/80 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/81 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/81 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/82 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/82 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/83 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/83 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/84 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/84 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/85 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/85 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/86 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/86 (42 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/87 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/87 (41 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/88 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/88 (43 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/89 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/89 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/90 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/90 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/91 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/91 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/92 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/92 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/93 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/93 (45 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/94 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/94 (44 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/95 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/95 (45 ms) 70: [----------] 96 tests from HBondTests/HbondModuleTest (3543 ms total) 70: 70: [----------] 4 tests from MoleculeTests/ScatteringModule 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (9 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (161 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (7 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (39 ms) 70: [----------] 4 tests from MoleculeTests/ScatteringModule (220 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 394 tests from 21 test suites ran. (6831 ms total) 70: [ PASSED ] 394 tests. 70/104 Test #70: TrajectoryAnalysisUnitTests ............... Passed 6.86 sec test 71 Start 71: EnergyAnalysisUnitTests 71: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests 71: Test timeout computed to be: 60 71: [==========] Running 12 tests from 5 test suites. 71: [----------] Global test environment set-up. 71: [----------] 2 tests from EnergyTermTest 71: [ RUN ] EnergyTermTest.ConstructWorks 71: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 71: [ RUN ] EnergyTermTest.AddFrameWorks 71: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 71: [----------] 2 tests from EnergyTermTest (0 ms total) 71: 71: [----------] 1 test from DhdlTest 71: [ RUN ] DhdlTest.ExtractDhdl 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 71: Note: file tpx version 110, software tpx version 138 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 71: 71: 71: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 71: [ OK ] DhdlTest.ExtractDhdl (14 ms) 71: [----------] 1 test from DhdlTest (15 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.ExtractOrires 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 71: Note: file tpx version 111, software tpx version 138 71: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 71: End your selection with 0 71: Selecting all 7 orientation restraints 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 71: [ OK ] OriresTest.ExtractOrires (12 ms) 71: [----------] 1 test from OriresTest (12 ms total) 71: 71: [----------] 5 tests from EnergyTest 71: [ RUN ] EnergyTest.ExtractEnergy 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: [ OK ] EnergyTest.ExtractEnergy (4 ms) 71: [ RUN ] EnergyTest.ExtractEnergyByNumber 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Pres. DC -268.49 3 8.52175 13.2804 (bar) 71: [ OK ] EnergyTest.ExtractEnergyByNumber (3 ms) 71: [ RUN ] EnergyTest.ExtractEnergyMixed 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: [ OK ] EnergyTest.ExtractEnergyMixed (4 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) 71: [----------] 5 tests from EnergyTest (16 ms total) 71: 71: [----------] 3 tests from ViscosityTest 71: [ RUN ] ViscosityTest.EinsteinViscosity 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosity (36 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityIntegral (43 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (28 ms) 71: [----------] 3 tests from ViscosityTest (108 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 5 test suites ran. (154 ms total) 71: [ PASSED ] 12 tests. 71/104 Test #71: EnergyAnalysisUnitTests ................... Passed 0.18 sec test 72 Start 72: ToolUnitTests 72: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/ToolUnitTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests 72: Test timeout computed to be: 1920 72: [==========] Running 70 tests from 8 test suites. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from DumpTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -1212488419 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] DumpTest.WorksWithTpr 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 72: inputrec: 72: integrator = md 72: tinit = 0 72: dt = 0.001 72: nsteps = 0 72: init-step = 0 72: simulation-part = 1 72: mts = false 72: mass-repartition-factor = 1 72: comm-mode = Linear 72: nstcomm = 100 72: bd-fric = 0 72: ld-seed = -1212488419 72: emtol = 10 72: emstep = 0.01 72: niter = 20 72: fcstep = 0 72: nstcgsteep = 1000 72: nbfgscorr = 10 72: rtpi = 0.05 72: nstxout = 0 72: nstvout = 0 72: nstfout = 0 72: nstlog = 1000 72: nstcalcenergy = 100 72: nstenergy = 1000 72: nstxout-compressed = 0 72: compressed-x-precision = 1000 72: cutoff-scheme = Verlet 72: nstlist = 10 72: pbc = xyz 72: periodic-molecules = false 72: verlet-buffer-tolerance = -1 72: verlet-buffer-pressure-tolerance = 0.5 72: rlist = 1.1 72: coulombtype = Cut-off 72: coulomb-modifier = Potential-shift 72: rcoulomb-switch = 0 72: rcoulomb = 1 72: epsilon-r = 1 72: epsilon-rf = inf 72: vdw-type = Cut-off 72: vdw-modifier = Potential-shift 72: rvdw-switch = 0 72: rvdw = 1 72: DispCorr = No 72: table-extension = 1 72: fourierspacing = 0.12 72: fourier-nx = 0 72: fourier-ny = 0 72: fourier-nz = 0 72: pme-order = 4 72: ewald-rtol = 1e-05 72: ewald-rtol-lj = 0.001 72: lj-pme-comb-rule = Geometric 72: ewald-geometry = 3d 72: epsilon-surface = 0 72: ensemble-temperature-setting = not available 72: tcoupl = No 72: nsttcouple = -1 72: nh-chain-length = 0 72: print-nose-hoover-chain-variables = false 72: pcoupl = No 72: refcoord-scaling = No 72: posres-com: not available 72: posres-comB: not available 72: QMMM = false 72: qm-opts: 72: ngQM = 0 72: constraint-algorithm = Lincs 72: continuation = false 72: Shake-SOR = false 72: shake-tol = 0.0001 72: lincs-order = 4 72: lincs-iter = 1 72: lincs-warnangle = 30 72: nwall = 0 72: wall-type = 9-3 72: wall-r-linpot = -1 72: wall-atomtype[0] = -1 72: wall-atomtype[1] = -1 72: wall-density[0] = 0 72: wall-density[1] = 0 72: wall-ewald-zfac = 3 72: pull = false 72: awh = false 72: rotation = false 72: interactiveMD = false 72: disre = No 72: disre-weighting = Conservative 72: disre-mixed = false 72: dr-fc = 1000 72: dr-tau = 0 72: nstdisreout = 100 72: orire-fc = 0 72: orire-tau = 0 72: nstorireout = 100 72: free-energy = no 72: cos-acceleration = 0 72: deform (3x3): 72: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: simulated-tempering = false 72: swapcoords = no 72: userint1 = 0 72: userint2 = 0 72: userint3 = 0 72: userint4 = 0 72: userreal1 = 0 72: userreal2 = 0 72: userreal3 = 0 72: userreal4 = 0 72: applied-forces: 72: electric-field: 72: x: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: y: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: z: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: density-guided-simulation: 72: active = false 72: group = protein 72: similarity-measure = inner-product 72: atom-spreading-weight = unity 72: force-constant = 1e+09 72: gaussian-transform-spreading-width = 0.2 72: gaussian-transform-spreading-range-in-multiples-of-width = 4 72: reference-density-filename = reference.mrc 72: nst = 1 72: normalize-densities = true 72: adaptive-force-scaling = false 72: adaptive-force-scaling-time-constant = 4 72: shift-vector = 72: transformation-matrix = 72: qmmm-cp2k: 72: active = false 72: qmgroup = System 72: qmmethod = PBE 72: qmfilenames = 72: qmcharge = 0 72: qmmultiplicity = 1 72: colvars: 72: active = false 72: configfile = 72: seed = -1 72: nnpot: 72: active = false 72: modelfile = model.pt 72: input-group = System 72: link-type = H 72: link-distance = 0.1 72: pair-cutoff = 0 72: embedding = mechanical 72: nnp-charge = 0 72: model-input1 = 72: model-input2 = 72: model-input3 = 72: model-input4 = 72: model-input5 = 72: model-input6 = 72: model-input7 = 72: model-input8 = 72: model-input9 = 72: fast-multipole-method: 72: fmm: 72: backend = inactive 72: exafmm-order = 6 72: exafmm-direct-range = 2 72: exafmm-direct-provider = GROMACS 72: exafmm-tree-type = uniform 72: exafmm-tree-depth = 0 72: exafmm-max-particles-per-cell = 0 72: fmsolvr-order = 8 72: fmsolvr-direct-range = 1 72: fmsolvr-direct-provider = FMM 72: fmsolvr-dipole-compensation = true 72: fmsolvr-tree-depth = 3 72: fmsolvr-sparse = false 72: grpopts: 72: nrdf: 465 72: ref-t: 0 72: tau-t: 0 72: annealing: No 72: annealing-npoints: 0 72: acc: 0 0 0 72: nfreeze: N N N 72: energygrp-flags[ 0]: 0 72: header: 72: bIr = present 72: bBox = present 72: bTop = present 72: bX = present 72: bV = present 72: bF = not present 72: natoms = 156 72: lambda = 0.000000e+00 72: buffer size = 47154 72: topology: 72: name="First 10 residues from 1AKI" 72: #atoms = 156 72: #molblock = 1 72: molblock (0): 72: moltype = 0 "Protein_chain_B" 72: #molecules = 1 72: #posres_xA = 0 72: #posres_xB = 0 72: bIntermolecularInteractions = false 72: ffparams: 72: atnr=10 72: ntypes=212 72: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 72: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 72: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 72: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 72: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 72: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 72: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 72: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 72: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 72: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 72: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 72: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 72: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 72: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 72: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 72: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 72: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 72: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 72: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 72: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 72: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 72: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 72: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 72: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 72: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 72: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 72: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 72: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 72: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 72: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 72: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 72: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 72: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 72: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 72: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 72: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 72: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 72: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 72: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 72: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 72: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 72: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 72: 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functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 72: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 72: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 72: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 72: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 72: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 72: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 72: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 72: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 72: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 72: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 72: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 72: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 72: functype[102]=BONDS, b0A= 1.09000e-01, 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functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 72: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 72: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 72: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 72: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 72: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 72: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 72: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 72: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 72: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 72: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 72: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 72: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 72: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 72: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 72: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 72: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 72: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 72: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 72: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 72: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 72: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 72: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 72: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 72: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 72: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 72: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 72: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 72: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 72: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 72: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 72: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 72: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 72: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 72: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 72: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 72: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 72: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 72: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 72: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 72: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 72: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 72: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 72: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 72: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 72: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 72: reppow = 12 72: fudgeQQ = 0.5 72: cmap 72: moltype (0): 72: name="Protein_chain_B" 72: atoms: 72: atom (156): 72: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 72: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 72: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 72: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 72: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 72: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 72: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 72: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 72: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 72: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 72: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 72: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 72: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 72: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 72: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 72: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 72: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 72: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 72: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 72: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 72: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 72: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 72: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 72: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 72: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 72: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 72: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 72: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 72: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 72: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 72: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 72: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 72: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 72: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 72: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 72: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 72: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 72: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 72: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 72: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 72: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 72: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 72: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 72: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 72: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 72: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 72: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 72: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 72: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 72: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 72: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 72: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 72: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 72: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 72: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 72: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 72: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 72: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 72: atom (156): 72: atom[0]={name="N"} 72: atom[1]={name="H1"} 72: atom[2]={name="H2"} 72: atom[3]={name="H3"} 72: atom[4]={name="CA"} 72: atom[5]={name="HA"} 72: atom[6]={name="CB"} 72: atom[7]={name="HB1"} 72: atom[8]={name="HB2"} 72: atom[9]={name="CG"} 72: atom[10]={name="HG1"} 72: atom[11]={name="HG2"} 72: atom[12]={name="CD"} 72: atom[13]={name="HD1"} 72: atom[14]={name="HD2"} 72: atom[15]={name="CE"} 72: atom[16]={name="HE1"} 72: atom[17]={name="HE2"} 72: atom[18]={name="NZ"} 72: atom[19]={name="HZ1"} 72: atom[20]={name="HZ2"} 72: atom[21]={name="HZ3"} 72: atom[22]={name="C"} 72: atom[23]={name="O"} 72: atom[24]={name="N"} 72: atom[25]={name="H"} 72: atom[26]={name="CA"} 72: atom[27]={name="HA"} 72: atom[28]={name="CB"} 72: atom[29]={name="HB"} 72: atom[30]={name="CG1"} 72: atom[31]={name="HG11"} 72: atom[32]={name="HG12"} 72: atom[33]={name="HG13"} 72: atom[34]={name="CG2"} 72: atom[35]={name="HG21"} 72: atom[36]={name="HG22"} 72: atom[37]={name="HG23"} 72: atom[38]={name="C"} 72: atom[39]={name="O"} 72: atom[40]={name="N"} 72: atom[41]={name="H"} 72: atom[42]={name="CA"} 72: atom[43]={name="HA"} 72: atom[44]={name="CB"} 72: atom[45]={name="HB1"} 72: atom[46]={name="HB2"} 72: atom[47]={name="CG"} 72: atom[48]={name="CD1"} 72: atom[49]={name="HD1"} 72: atom[50]={name="CD2"} 72: atom[51]={name="HD2"} 72: atom[52]={name="CE1"} 72: atom[53]={name="HE1"} 72: atom[54]={name="CE2"} 72: atom[55]={name="HE2"} 72: atom[56]={name="CZ"} 72: atom[57]={name="HZ"} 72: atom[58]={name="C"} 72: atom[59]={name="O"} 72: atom[60]={name="N"} 72: atom[61]={name="H"} 72: atom[62]={name="CA"} 72: atom[63]={name="HA1"} 72: atom[64]={name="HA2"} 72: atom[65]={name="C"} 72: atom[66]={name="O"} 72: atom[67]={name="N"} 72: atom[68]={name="H"} 72: atom[69]={name="CA"} 72: atom[70]={name="HA"} 72: atom[71]={name="CB"} 72: atom[72]={name="HB1"} 72: atom[73]={name="HB2"} 72: atom[74]={name="CG"} 72: atom[75]={name="HG1"} 72: atom[76]={name="HG2"} 72: atom[77]={name="CD"} 72: atom[78]={name="HD1"} 72: atom[79]={name="HD2"} 72: atom[80]={name="NE"} 72: atom[81]={name="HE"} 72: atom[82]={name="CZ"} 72: atom[83]={name="NH1"} 72: atom[84]={name="HH11"} 72: atom[85]={name="HH12"} 72: atom[86]={name="NH2"} 72: atom[87]={name="HH21"} 72: atom[88]={name="HH22"} 72: atom[89]={name="C"} 72: atom[90]={name="O"} 72: atom[91]={name="N"} 72: atom[92]={name="H"} 72: atom[93]={name="CA"} 72: atom[94]={name="HA"} 72: atom[95]={name="CB"} 72: atom[96]={name="HB1"} 72: atom[97]={name="HB2"} 72: atom[98]={name="SG"} 72: atom[99]={name="HG"} 72: atom[100]={name="C"} 72: atom[101]={name="O"} 72: atom[102]={name="N"} 72: atom[103]={name="H"} 72: atom[104]={name="CA"} 72: atom[105]={name="HA"} 72: atom[106]={name="CB"} 72: atom[107]={name="HB1"} 72: atom[108]={name="HB2"} 72: atom[109]={name="CG"} 72: atom[110]={name="HG1"} 72: atom[111]={name="HG2"} 72: atom[112]={name="CD"} 72: atom[113]={name="OE1"} 72: atom[114]={name="OE2"} 72: atom[115]={name="C"} 72: atom[116]={name="O"} 72: atom[117]={name="N"} 72: atom[118]={name="H"} 72: atom[119]={name="CA"} 72: atom[120]={name="HA"} 72: atom[121]={name="CB"} 72: atom[122]={name="HB1"} 72: atom[123]={name="HB2"} 72: atom[124]={name="CG"} 72: atom[125]={name="HG"} 72: atom[126]={name="CD1"} 72: atom[127]={name="HD11"} 72: atom[128]={name="HD12"} 72: atom[129]={name="HD13"} 72: atom[130]={name="CD2"} 72: atom[131]={name="HD21"} 72: atom[132]={name="HD22"} 72: atom[133]={name="HD23"} 72: atom[134]={name="C"} 72: atom[135]={name="O"} 72: atom[136]={name="N"} 72: atom[137]={name="H"} 72: atom[138]={name="CA"} 72: atom[139]={name="HA"} 72: atom[140]={name="CB"} 72: atom[141]={name="HB1"} 72: atom[142]={name="HB2"} 72: atom[143]={name="HB3"} 72: atom[144]={name="C"} 72: atom[145]={name="O"} 72: atom[146]={name="N"} 72: atom[147]={name="H"} 72: atom[148]={name="CA"} 72: atom[149]={name="HA"} 72: atom[150]={name="CB"} 72: atom[151]={name="HB1"} 72: atom[152]={name="HB2"} 72: atom[153]={name="HB3"} 72: atom[154]={name="C"} 72: atom[155]={name="O"} 72: type (156): 72: type[0]={name="opls_287",nameB="opls_287"} 72: type[1]={name="opls_290",nameB="opls_290"} 72: type[2]={name="opls_290",nameB="opls_290"} 72: type[3]={name="opls_290",nameB="opls_290"} 72: type[4]={name="opls_293B",nameB="opls_293B"} 72: type[5]={name="opls_140",nameB="opls_140"} 72: type[6]={name="opls_136",nameB="opls_136"} 72: type[7]={name="opls_140",nameB="opls_140"} 72: type[8]={name="opls_140",nameB="opls_140"} 72: type[9]={name="opls_136",nameB="opls_136"} 72: type[10]={name="opls_140",nameB="opls_140"} 72: type[11]={name="opls_140",nameB="opls_140"} 72: type[12]={name="opls_136",nameB="opls_136"} 72: type[13]={name="opls_140",nameB="opls_140"} 72: type[14]={name="opls_140",nameB="opls_140"} 72: type[15]={name="opls_292",nameB="opls_292"} 72: type[16]={name="opls_140",nameB="opls_140"} 72: type[17]={name="opls_140",nameB="opls_140"} 72: type[18]={name="opls_287",nameB="opls_287"} 72: type[19]={name="opls_290",nameB="opls_290"} 72: type[20]={name="opls_290",nameB="opls_290"} 72: type[21]={name="opls_290",nameB="opls_290"} 72: type[22]={name="opls_235",nameB="opls_235"} 72: type[23]={name="opls_236",nameB="opls_236"} 72: type[24]={name="opls_238",nameB="opls_238"} 72: type[25]={name="opls_241",nameB="opls_241"} 72: type[26]={name="opls_224B",nameB="opls_224B"} 72: type[27]={name="opls_140",nameB="opls_140"} 72: type[28]={name="opls_137",nameB="opls_137"} 72: type[29]={name="opls_140",nameB="opls_140"} 72: type[30]={name="opls_135",nameB="opls_135"} 72: type[31]={name="opls_140",nameB="opls_140"} 72: type[32]={name="opls_140",nameB="opls_140"} 72: type[33]={name="opls_140",nameB="opls_140"} 72: type[34]={name="opls_135",nameB="opls_135"} 72: type[35]={name="opls_140",nameB="opls_140"} 72: type[36]={name="opls_140",nameB="opls_140"} 72: type[37]={name="opls_140",nameB="opls_140"} 72: type[38]={name="opls_235",nameB="opls_235"} 72: type[39]={name="opls_236",nameB="opls_236"} 72: type[40]={name="opls_238",nameB="opls_238"} 72: type[41]={name="opls_241",nameB="opls_241"} 72: type[42]={name="opls_224B",nameB="opls_224B"} 72: type[43]={name="opls_140",nameB="opls_140"} 72: type[44]={name="opls_149",nameB="opls_149"} 72: type[45]={name="opls_140",nameB="opls_140"} 72: type[46]={name="opls_140",nameB="opls_140"} 72: type[47]={name="opls_145",nameB="opls_145"} 72: type[48]={name="opls_145",nameB="opls_145"} 72: type[49]={name="opls_146",nameB="opls_146"} 72: type[50]={name="opls_145",nameB="opls_145"} 72: type[51]={name="opls_146",nameB="opls_146"} 72: type[52]={name="opls_145",nameB="opls_145"} 72: type[53]={name="opls_146",nameB="opls_146"} 72: type[54]={name="opls_145",nameB="opls_145"} 72: type[55]={name="opls_146",nameB="opls_146"} 72: type[56]={name="opls_145",nameB="opls_145"} 72: type[57]={name="opls_146",nameB="opls_146"} 72: type[58]={name="opls_235",nameB="opls_235"} 72: type[59]={name="opls_236",nameB="opls_236"} 72: type[60]={name="opls_238",nameB="opls_238"} 72: type[61]={name="opls_241",nameB="opls_241"} 72: type[62]={name="opls_223B",nameB="opls_223B"} 72: type[63]={name="opls_140",nameB="opls_140"} 72: type[64]={name="opls_140",nameB="opls_140"} 72: type[65]={name="opls_235",nameB="opls_235"} 72: type[66]={name="opls_236",nameB="opls_236"} 72: type[67]={name="opls_238",nameB="opls_238"} 72: type[68]={name="opls_241",nameB="opls_241"} 72: type[69]={name="opls_224B",nameB="opls_224B"} 72: type[70]={name="opls_140",nameB="opls_140"} 72: type[71]={name="opls_136",nameB="opls_136"} 72: type[72]={name="opls_140",nameB="opls_140"} 72: type[73]={name="opls_140",nameB="opls_140"} 72: type[74]={name="opls_308",nameB="opls_308"} 72: type[75]={name="opls_140",nameB="opls_140"} 72: type[76]={name="opls_140",nameB="opls_140"} 72: type[77]={name="opls_307",nameB="opls_307"} 72: type[78]={name="opls_140",nameB="opls_140"} 72: type[79]={name="opls_140",nameB="opls_140"} 72: type[80]={name="opls_303",nameB="opls_303"} 72: type[81]={name="opls_304",nameB="opls_304"} 72: type[82]={name="opls_302",nameB="opls_302"} 72: type[83]={name="opls_300",nameB="opls_300"} 72: type[84]={name="opls_301",nameB="opls_301"} 72: type[85]={name="opls_301",nameB="opls_301"} 72: type[86]={name="opls_300",nameB="opls_300"} 72: type[87]={name="opls_301",nameB="opls_301"} 72: type[88]={name="opls_301",nameB="opls_301"} 72: type[89]={name="opls_235",nameB="opls_235"} 72: type[90]={name="opls_236",nameB="opls_236"} 72: type[91]={name="opls_238",nameB="opls_238"} 72: type[92]={name="opls_241",nameB="opls_241"} 72: type[93]={name="opls_224B",nameB="opls_224B"} 72: type[94]={name="opls_140",nameB="opls_140"} 72: type[95]={name="opls_206",nameB="opls_206"} 72: type[96]={name="opls_140",nameB="opls_140"} 72: type[97]={name="opls_140",nameB="opls_140"} 72: type[98]={name="opls_200",nameB="opls_200"} 72: type[99]={name="opls_204",nameB="opls_204"} 72: type[100]={name="opls_235",nameB="opls_235"} 72: type[101]={name="opls_236",nameB="opls_236"} 72: type[102]={name="opls_238",nameB="opls_238"} 72: type[103]={name="opls_241",nameB="opls_241"} 72: type[104]={name="opls_224B",nameB="opls_224B"} 72: type[105]={name="opls_140",nameB="opls_140"} 72: type[106]={name="opls_136",nameB="opls_136"} 72: type[107]={name="opls_140",nameB="opls_140"} 72: type[108]={name="opls_140",nameB="opls_140"} 72: type[109]={name="opls_274",nameB="opls_274"} 72: type[110]={name="opls_140",nameB="opls_140"} 72: type[111]={name="opls_140",nameB="opls_140"} 72: type[112]={name="opls_271",nameB="opls_271"} 72: type[113]={name="opls_272",nameB="opls_272"} 72: type[114]={name="opls_272",nameB="opls_272"} 72: type[115]={name="opls_235",nameB="opls_235"} 72: type[116]={name="opls_236",nameB="opls_236"} 72: type[117]={name="opls_238",nameB="opls_238"} 72: type[118]={name="opls_241",nameB="opls_241"} 72: type[119]={name="opls_224B",nameB="opls_224B"} 72: type[120]={name="opls_140",nameB="opls_140"} 72: type[121]={name="opls_136",nameB="opls_136"} 72: type[122]={name="opls_140",nameB="opls_140"} 72: type[123]={name="opls_140",nameB="opls_140"} 72: type[124]={name="opls_137",nameB="opls_137"} 72: type[125]={name="opls_140",nameB="opls_140"} 72: type[126]={name="opls_135",nameB="opls_135"} 72: type[127]={name="opls_140",nameB="opls_140"} 72: type[128]={name="opls_140",nameB="opls_140"} 72: type[129]={name="opls_140",nameB="opls_140"} 72: type[130]={name="opls_135",nameB="opls_135"} 72: type[131]={name="opls_140",nameB="opls_140"} 72: type[132]={name="opls_140",nameB="opls_140"} 72: type[133]={name="opls_140",nameB="opls_140"} 72: type[134]={name="opls_235",nameB="opls_235"} 72: type[135]={name="opls_236",nameB="opls_236"} 72: type[136]={name="opls_238",nameB="opls_238"} 72: type[137]={name="opls_241",nameB="opls_241"} 72: type[138]={name="opls_224B",nameB="opls_224B"} 72: type[139]={name="opls_140",nameB="opls_140"} 72: type[140]={name="opls_135",nameB="opls_135"} 72: type[141]={name="opls_140",nameB="opls_140"} 72: type[142]={name="opls_140",nameB="opls_140"} 72: type[143]={name="opls_140",nameB="opls_140"} 72: type[144]={name="opls_235",nameB="opls_235"} 72: type[145]={name="opls_236",nameB="opls_236"} 72: type[146]={name="opls_238",nameB="opls_238"} 72: type[147]={name="opls_241",nameB="opls_241"} 72: type[148]={name="opls_224B",nameB="opls_224B"} 72: type[149]={name="opls_140",nameB="opls_140"} 72: type[150]={name="opls_135",nameB="opls_135"} 72: type[151]={name="opls_140",nameB="opls_140"} 72: type[152]={name="opls_140",nameB="opls_140"} 72: type[153]={name="opls_140",nameB="opls_140"} 72: type[154]={name="opls_235",nameB="opls_235"} 72: type[155]={name="opls_236",nameB="opls_236"} 72: residue (10): 72: residue[0]={name="LYS", nr=1, ic=' '} 72: residue[1]={name="VAL", nr=2, ic=' '} 72: residue[2]={name="PHE", nr=3, ic=' '} 72: residue[3]={name="GLY", nr=4, ic=' '} 72: residue[4]={name="ARG", nr=5, ic=' '} 72: residue[5]={name="CYS", nr=6, ic=' '} 72: residue[6]={name="GLU", nr=7, ic=' '} 72: residue[7]={name="LEU", nr=8, ic=' '} 72: residue[8]={name="ALA", nr=9, ic=' '} 72: residue[9]={name="ALA", nr=10, ic=' '} 72: excls: 72: numLists=156 72: numElements=1828 72: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 72: 23, 24, 25, 26} 72: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 72: 14, 15, 22, 23, 24} 72: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 72: 16, 17, 18, 22} 72: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 72: 17, 18, 19, 20, 21} 72: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 72: 20, 21} 72: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 72: 26, 27, 28, 38} 72: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 72: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 72: 30, 34, 38, 39, 40} 72: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 72: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 72: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 72: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40} 72: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 72: 34, 35, 36, 37, 38, 39, 40} 72: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40, 41, 42, 43, 44, 58} 72: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 72: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 72: 45, 46, 47, 58, 59, 60} 72: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 72: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 72: 48, 50, 58, 59, 60, 61, 62} 72: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60} 72: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 72: 50, 51, 52, 54, 58, 59, 60} 72: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 72: 52, 53, 54, 55, 56, 58} 72: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 72: 54, 56, 57} 72: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 72: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 72: 55, 56, 57} 72: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 72: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 72: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 72: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 72: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 72: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60, 61, 62, 63, 64, 65} 72: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 72: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 72: 65, 66, 67} 72: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 72: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 72: 68, 69} 72: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72: 70, 71, 89} 72: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 72: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72: 72, 73, 74, 89, 90, 91} 72: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 72: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 72: 75, 76, 77, 89, 90, 91, 92, 93} 72: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91} 72: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 72: 77, 78, 79, 80, 89, 90, 91} 72: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 72: 79, 80, 81, 82, 89} 72: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 72: 81, 82, 83, 86} 72: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 72: 84, 85, 86, 87, 88} 72: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 72: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 72: 87, 88} 72: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[84][num=6]={80, 82, 83, 84, 85, 86} 72: excls[85][num=6]={80, 82, 83, 84, 85, 86} 72: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[87][num=6]={80, 82, 83, 86, 87, 88} 72: excls[88][num=6]={80, 82, 83, 86, 87, 88} 72: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91, 92, 93, 94, 95, 100} 72: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 72: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 72: 96, 97, 98, 100, 101, 102} 72: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 72: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 72: 99, 100, 101, 102, 103, 104} 72: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102} 72: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 72: 101, 102} 72: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[99][num=6]={93, 95, 96, 97, 98, 99} 72: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102, 103, 104, 105, 106, 115} 72: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 72: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 72: 106, 107, 108, 109, 115, 116, 117} 72: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 72: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 72: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 72: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117} 72: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 110, 111, 112, 113, 114, 115, 116, 117} 72: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 113, 114, 115} 72: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 72: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 72: 120, 121, 122, 123, 124, 134, 135, 136} 72: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 72: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 72: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136} 72: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 72: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 127, 128, 129, 130, 131, 132, 133, 134} 72: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 72: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 72: 139, 140, 141, 142, 143, 144, 145, 146} 72: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 72: 142, 143, 144, 145, 146, 147, 148} 72: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 72: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 72: 149, 150, 151, 152, 153, 154, 155} 72: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 72: 152, 153, 154, 155} 72: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[155][num=6]={146, 148, 149, 150, 154, 155} 72: Bond: 72: nr: 468 72: iatoms: 72: 0 type=100 (BONDS) 0 1 72: 1 type=100 (BONDS) 0 2 72: 2 type=100 (BONDS) 0 3 72: 3 type=101 (BONDS) 0 4 72: 4 type=102 (BONDS) 4 5 72: 5 type=103 (BONDS) 4 6 72: 6 type=104 (BONDS) 4 22 72: 7 type=102 (BONDS) 6 7 72: 8 type=102 (BONDS) 6 8 72: 9 type=103 (BONDS) 6 9 72: 10 type=102 (BONDS) 9 10 72: 11 type=102 (BONDS) 9 11 72: 12 type=103 (BONDS) 9 12 72: 13 type=102 (BONDS) 12 13 72: 14 type=102 (BONDS) 12 14 72: 15 type=103 (BONDS) 12 15 72: 16 type=102 (BONDS) 15 16 72: 17 type=102 (BONDS) 15 17 72: 18 type=101 (BONDS) 15 18 72: 19 type=100 (BONDS) 18 19 72: 20 type=100 (BONDS) 18 20 72: 21 type=100 (BONDS) 18 21 72: 22 type=105 (BONDS) 22 23 72: 23 type=106 (BONDS) 22 24 72: 24 type=100 (BONDS) 24 25 72: 25 type=107 (BONDS) 24 26 72: 26 type=102 (BONDS) 26 27 72: 27 type=103 (BONDS) 26 28 72: 28 type=104 (BONDS) 26 38 72: 29 type=102 (BONDS) 28 29 72: 30 type=103 (BONDS) 28 30 72: 31 type=103 (BONDS) 28 34 72: 32 type=102 (BONDS) 30 31 72: 33 type=102 (BONDS) 30 32 72: 34 type=102 (BONDS) 30 33 72: 35 type=102 (BONDS) 34 35 72: 36 type=102 (BONDS) 34 36 72: 37 type=102 (BONDS) 34 37 72: 38 type=105 (BONDS) 38 39 72: 39 type=106 (BONDS) 38 40 72: 40 type=100 (BONDS) 40 41 72: 41 type=107 (BONDS) 40 42 72: 42 type=102 (BONDS) 42 43 72: 43 type=103 (BONDS) 42 44 72: 44 type=104 (BONDS) 42 58 72: 45 type=102 (BONDS) 44 45 72: 46 type=102 (BONDS) 44 46 72: 47 type=108 (BONDS) 44 47 72: 48 type=109 (BONDS) 47 48 72: 49 type=109 (BONDS) 47 50 72: 50 type=110 (BONDS) 48 49 72: 51 type=109 (BONDS) 48 52 72: 52 type=110 (BONDS) 50 51 72: 53 type=109 (BONDS) 50 54 72: 54 type=110 (BONDS) 52 53 72: 55 type=109 (BONDS) 52 56 72: 56 type=110 (BONDS) 54 55 72: 57 type=109 (BONDS) 54 56 72: 58 type=110 (BONDS) 56 57 72: 59 type=105 (BONDS) 58 59 72: 60 type=106 (BONDS) 58 60 72: 61 type=100 (BONDS) 60 61 72: 62 type=107 (BONDS) 60 62 72: 63 type=102 (BONDS) 62 63 72: 64 type=102 (BONDS) 62 64 72: 65 type=104 (BONDS) 62 65 72: 66 type=105 (BONDS) 65 66 72: 67 type=106 (BONDS) 65 67 72: 68 type=100 (BONDS) 67 68 72: 69 type=107 (BONDS) 67 69 72: 70 type=102 (BONDS) 69 70 72: 71 type=103 (BONDS) 69 71 72: 72 type=104 (BONDS) 69 89 72: 73 type=102 (BONDS) 71 72 72: 74 type=102 (BONDS) 71 73 72: 75 type=103 (BONDS) 71 74 72: 76 type=102 (BONDS) 74 75 72: 77 type=102 (BONDS) 74 76 72: 78 type=103 (BONDS) 74 77 72: 79 type=102 (BONDS) 77 78 72: 80 type=102 (BONDS) 77 79 72: 81 type=111 (BONDS) 77 80 72: 82 type=100 (BONDS) 80 81 72: 83 type=112 (BONDS) 80 82 72: 84 type=112 (BONDS) 82 83 72: 85 type=112 (BONDS) 82 86 72: 86 type=100 (BONDS) 83 84 72: 87 type=100 (BONDS) 83 85 72: 88 type=100 (BONDS) 86 87 72: 89 type=100 (BONDS) 86 88 72: 90 type=105 (BONDS) 89 90 72: 91 type=106 (BONDS) 89 91 72: 92 type=100 (BONDS) 91 92 72: 93 type=107 (BONDS) 91 93 72: 94 type=102 (BONDS) 93 94 72: 95 type=103 (BONDS) 93 95 72: 96 type=104 (BONDS) 93 100 72: 97 type=102 (BONDS) 95 96 72: 98 type=102 (BONDS) 95 97 72: 99 type=113 (BONDS) 95 98 72: 100 type=114 (BONDS) 98 99 72: 101 type=105 (BONDS) 100 101 72: 102 type=106 (BONDS) 100 102 72: 103 type=100 (BONDS) 102 103 72: 104 type=107 (BONDS) 102 104 72: 105 type=102 (BONDS) 104 105 72: 106 type=103 (BONDS) 104 106 72: 107 type=104 (BONDS) 104 115 72: 108 type=102 (BONDS) 106 107 72: 109 type=102 (BONDS) 106 108 72: 110 type=103 (BONDS) 106 109 72: 111 type=102 (BONDS) 109 110 72: 112 type=102 (BONDS) 109 111 72: 113 type=104 (BONDS) 109 112 72: 114 type=115 (BONDS) 112 113 72: 115 type=115 (BONDS) 112 114 72: 116 type=105 (BONDS) 115 116 72: 117 type=106 (BONDS) 115 117 72: 118 type=100 (BONDS) 117 118 72: 119 type=107 (BONDS) 117 119 72: 120 type=102 (BONDS) 119 120 72: 121 type=103 (BONDS) 119 121 72: 122 type=104 (BONDS) 119 134 72: 123 type=102 (BONDS) 121 122 72: 124 type=102 (BONDS) 121 123 72: 125 type=103 (BONDS) 121 124 72: 126 type=102 (BONDS) 124 125 72: 127 type=103 (BONDS) 124 126 72: 128 type=103 (BONDS) 124 130 72: 129 type=102 (BONDS) 126 127 72: 130 type=102 (BONDS) 126 128 72: 131 type=102 (BONDS) 126 129 72: 132 type=102 (BONDS) 130 131 72: 133 type=102 (BONDS) 130 132 72: 134 type=102 (BONDS) 130 133 72: 135 type=105 (BONDS) 134 135 72: 136 type=106 (BONDS) 134 136 72: 137 type=100 (BONDS) 136 137 72: 138 type=107 (BONDS) 136 138 72: 139 type=102 (BONDS) 138 139 72: 140 type=103 (BONDS) 138 140 72: 141 type=104 (BONDS) 138 144 72: 142 type=102 (BONDS) 140 141 72: 143 type=102 (BONDS) 140 142 72: 144 type=102 (BONDS) 140 143 72: 145 type=105 (BONDS) 144 145 72: 146 type=106 (BONDS) 144 146 72: 147 type=100 (BONDS) 146 147 72: 148 type=107 (BONDS) 146 148 72: 149 type=102 (BONDS) 148 149 72: 150 type=103 (BONDS) 148 150 72: 151 type=104 (BONDS) 148 154 72: 152 type=102 (BONDS) 150 151 72: 153 type=102 (BONDS) 150 152 72: 154 type=102 (BONDS) 150 153 72: 155 type=105 (BONDS) 154 155 72: G96Bond: 72: nr: 0 72: Morse: 72: nr: 0 72: Cubic Bonds: 72: nr: 0 72: Connect Bonds: 72: nr: 0 72: Harmonic Pot.: 72: nr: 0 72: FENE Bonds: 72: nr: 0 72: Tab. Bonds: 72: nr: 0 72: Tab. Bonds NC: 72: nr: 0 72: Restraint Pot.: 72: nr: 0 72: Angle: 72: nr: 1124 72: iatoms: 72: 0 type=116 (ANGLES) 1 0 2 72: 1 type=116 (ANGLES) 1 0 3 72: 2 type=116 (ANGLES) 1 0 4 72: 3 type=116 (ANGLES) 2 0 3 72: 4 type=116 (ANGLES) 2 0 4 72: 5 type=116 (ANGLES) 3 0 4 72: 6 type=116 (ANGLES) 0 4 5 72: 7 type=117 (ANGLES) 0 4 6 72: 8 type=117 (ANGLES) 0 4 22 72: 9 type=118 (ANGLES) 5 4 6 72: 10 type=116 (ANGLES) 5 4 22 72: 11 type=119 (ANGLES) 6 4 22 72: 12 type=118 (ANGLES) 4 6 7 72: 13 type=118 (ANGLES) 4 6 8 72: 14 type=120 (ANGLES) 4 6 9 72: 15 type=121 (ANGLES) 7 6 8 72: 16 type=118 (ANGLES) 7 6 9 72: 17 type=118 (ANGLES) 8 6 9 72: 18 type=118 (ANGLES) 6 9 10 72: 19 type=118 (ANGLES) 6 9 11 72: 20 type=120 (ANGLES) 6 9 12 72: 21 type=121 (ANGLES) 10 9 11 72: 22 type=118 (ANGLES) 10 9 12 72: 23 type=118 (ANGLES) 11 9 12 72: 24 type=118 (ANGLES) 9 12 13 72: 25 type=118 (ANGLES) 9 12 14 72: 26 type=120 (ANGLES) 9 12 15 72: 27 type=121 (ANGLES) 13 12 14 72: 28 type=118 (ANGLES) 13 12 15 72: 29 type=118 (ANGLES) 14 12 15 72: 30 type=118 (ANGLES) 12 15 16 72: 31 type=118 (ANGLES) 12 15 17 72: 32 type=117 (ANGLES) 12 15 18 72: 33 type=121 (ANGLES) 16 15 17 72: 34 type=116 (ANGLES) 16 15 18 72: 35 type=116 (ANGLES) 17 15 18 72: 36 type=116 (ANGLES) 15 18 19 72: 37 type=116 (ANGLES) 15 18 20 72: 38 type=116 (ANGLES) 15 18 21 72: 39 type=116 (ANGLES) 19 18 20 72: 40 type=116 (ANGLES) 19 18 21 72: 41 type=116 (ANGLES) 20 18 21 72: 42 type=122 (ANGLES) 4 22 23 72: 43 type=123 (ANGLES) 4 22 24 72: 44 type=124 (ANGLES) 23 22 24 72: 45 type=125 (ANGLES) 22 24 25 72: 46 type=126 (ANGLES) 22 24 26 72: 47 type=127 (ANGLES) 25 24 26 72: 48 type=116 (ANGLES) 24 26 27 72: 49 type=128 (ANGLES) 24 26 28 72: 50 type=129 (ANGLES) 24 26 38 72: 51 type=118 (ANGLES) 27 26 28 72: 52 type=116 (ANGLES) 27 26 38 72: 53 type=119 (ANGLES) 28 26 38 72: 54 type=118 (ANGLES) 26 28 29 72: 55 type=120 (ANGLES) 26 28 30 72: 56 type=120 (ANGLES) 26 28 34 72: 57 type=118 (ANGLES) 29 28 30 72: 58 type=118 (ANGLES) 29 28 34 72: 59 type=120 (ANGLES) 30 28 34 72: 60 type=118 (ANGLES) 28 30 31 72: 61 type=118 (ANGLES) 28 30 32 72: 62 type=118 (ANGLES) 28 30 33 72: 63 type=121 (ANGLES) 31 30 32 72: 64 type=121 (ANGLES) 31 30 33 72: 65 type=121 (ANGLES) 32 30 33 72: 66 type=118 (ANGLES) 28 34 35 72: 67 type=118 (ANGLES) 28 34 36 72: 68 type=118 (ANGLES) 28 34 37 72: 69 type=121 (ANGLES) 35 34 36 72: 70 type=121 (ANGLES) 35 34 37 72: 71 type=121 (ANGLES) 36 34 37 72: 72 type=122 (ANGLES) 26 38 39 72: 73 type=123 (ANGLES) 26 38 40 72: 74 type=124 (ANGLES) 39 38 40 72: 75 type=125 (ANGLES) 38 40 41 72: 76 type=126 (ANGLES) 38 40 42 72: 77 type=127 (ANGLES) 41 40 42 72: 78 type=116 (ANGLES) 40 42 43 72: 79 type=128 (ANGLES) 40 42 44 72: 80 type=129 (ANGLES) 40 42 58 72: 81 type=118 (ANGLES) 43 42 44 72: 82 type=116 (ANGLES) 43 42 58 72: 83 type=119 (ANGLES) 44 42 58 72: 84 type=118 (ANGLES) 42 44 45 72: 85 type=118 (ANGLES) 42 44 46 72: 86 type=130 (ANGLES) 42 44 47 72: 87 type=121 (ANGLES) 45 44 46 72: 88 type=116 (ANGLES) 45 44 47 72: 89 type=116 (ANGLES) 46 44 47 72: 90 type=131 (ANGLES) 44 47 48 72: 91 type=131 (ANGLES) 44 47 50 72: 92 type=132 (ANGLES) 48 47 50 72: 93 type=133 (ANGLES) 47 48 49 72: 94 type=132 (ANGLES) 47 48 52 72: 95 type=133 (ANGLES) 49 48 52 72: 96 type=133 (ANGLES) 47 50 51 72: 97 type=132 (ANGLES) 47 50 54 72: 98 type=133 (ANGLES) 51 50 54 72: 99 type=133 (ANGLES) 48 52 53 72: 100 type=132 (ANGLES) 48 52 56 72: 101 type=133 (ANGLES) 53 52 56 72: 102 type=133 (ANGLES) 50 54 55 72: 103 type=132 (ANGLES) 50 54 56 72: 104 type=133 (ANGLES) 55 54 56 72: 105 type=132 (ANGLES) 52 56 54 72: 106 type=133 (ANGLES) 52 56 57 72: 107 type=133 (ANGLES) 54 56 57 72: 108 type=122 (ANGLES) 42 58 59 72: 109 type=123 (ANGLES) 42 58 60 72: 110 type=124 (ANGLES) 59 58 60 72: 111 type=125 (ANGLES) 58 60 61 72: 112 type=126 (ANGLES) 58 60 62 72: 113 type=127 (ANGLES) 61 60 62 72: 114 type=116 (ANGLES) 60 62 63 72: 115 type=116 (ANGLES) 60 62 64 72: 116 type=129 (ANGLES) 60 62 65 72: 117 type=121 (ANGLES) 63 62 64 72: 118 type=116 (ANGLES) 63 62 65 72: 119 type=116 (ANGLES) 64 62 65 72: 120 type=122 (ANGLES) 62 65 66 72: 121 type=123 (ANGLES) 62 65 67 72: 122 type=124 (ANGLES) 66 65 67 72: 123 type=125 (ANGLES) 65 67 68 72: 124 type=126 (ANGLES) 65 67 69 72: 125 type=127 (ANGLES) 68 67 69 72: 126 type=116 (ANGLES) 67 69 70 72: 127 type=128 (ANGLES) 67 69 71 72: 128 type=129 (ANGLES) 67 69 89 72: 129 type=118 (ANGLES) 70 69 71 72: 130 type=116 (ANGLES) 70 69 89 72: 131 type=119 (ANGLES) 71 69 89 72: 132 type=118 (ANGLES) 69 71 72 72: 133 type=118 (ANGLES) 69 71 73 72: 134 type=120 (ANGLES) 69 71 74 72: 135 type=121 (ANGLES) 72 71 73 72: 136 type=118 (ANGLES) 72 71 74 72: 137 type=118 (ANGLES) 73 71 74 72: 138 type=118 (ANGLES) 71 74 75 72: 139 type=118 (ANGLES) 71 74 76 72: 140 type=120 (ANGLES) 71 74 77 72: 141 type=121 (ANGLES) 75 74 76 72: 142 type=118 (ANGLES) 75 74 77 72: 143 type=118 (ANGLES) 76 74 77 72: 144 type=118 (ANGLES) 74 77 78 72: 145 type=118 (ANGLES) 74 77 79 72: 146 type=117 (ANGLES) 74 77 80 72: 147 type=121 (ANGLES) 78 77 79 72: 148 type=116 (ANGLES) 78 77 80 72: 149 type=116 (ANGLES) 79 77 80 72: 150 type=134 (ANGLES) 77 80 81 72: 151 type=135 (ANGLES) 77 80 82 72: 152 type=133 (ANGLES) 81 80 82 72: 153 type=131 (ANGLES) 80 82 83 72: 154 type=131 (ANGLES) 80 82 86 72: 155 type=131 (ANGLES) 83 82 86 72: 156 type=133 (ANGLES) 82 83 84 72: 157 type=133 (ANGLES) 82 83 85 72: 158 type=133 (ANGLES) 84 83 85 72: 159 type=133 (ANGLES) 82 86 87 72: 160 type=133 (ANGLES) 82 86 88 72: 161 type=133 (ANGLES) 87 86 88 72: 162 type=122 (ANGLES) 69 89 90 72: 163 type=123 (ANGLES) 69 89 91 72: 164 type=124 (ANGLES) 90 89 91 72: 165 type=125 (ANGLES) 89 91 92 72: 166 type=126 (ANGLES) 89 91 93 72: 167 type=127 (ANGLES) 92 91 93 72: 168 type=116 (ANGLES) 91 93 94 72: 169 type=128 (ANGLES) 91 93 95 72: 170 type=129 (ANGLES) 91 93 100 72: 171 type=118 (ANGLES) 94 93 95 72: 172 type=116 (ANGLES) 94 93 100 72: 173 type=119 (ANGLES) 95 93 100 72: 174 type=118 (ANGLES) 93 95 96 72: 175 type=118 (ANGLES) 93 95 97 72: 176 type=136 (ANGLES) 93 95 98 72: 177 type=121 (ANGLES) 96 95 97 72: 178 type=116 (ANGLES) 96 95 98 72: 179 type=116 (ANGLES) 97 95 98 72: 180 type=137 (ANGLES) 95 98 99 72: 181 type=122 (ANGLES) 93 100 101 72: 182 type=123 (ANGLES) 93 100 102 72: 183 type=124 (ANGLES) 101 100 102 72: 184 type=125 (ANGLES) 100 102 103 72: 185 type=126 (ANGLES) 100 102 104 72: 186 type=127 (ANGLES) 103 102 104 72: 187 type=116 (ANGLES) 102 104 105 72: 188 type=128 (ANGLES) 102 104 106 72: 189 type=129 (ANGLES) 102 104 115 72: 190 type=118 (ANGLES) 105 104 106 72: 191 type=116 (ANGLES) 105 104 115 72: 192 type=119 (ANGLES) 106 104 115 72: 193 type=118 (ANGLES) 104 106 107 72: 194 type=118 (ANGLES) 104 106 108 72: 195 type=120 (ANGLES) 104 106 109 72: 196 type=121 (ANGLES) 107 106 108 72: 197 type=118 (ANGLES) 107 106 109 72: 198 type=118 (ANGLES) 108 106 109 72: 199 type=118 (ANGLES) 106 109 110 72: 200 type=118 (ANGLES) 106 109 111 72: 201 type=119 (ANGLES) 106 109 112 72: 202 type=121 (ANGLES) 110 109 111 72: 203 type=116 (ANGLES) 110 109 112 72: 204 type=116 (ANGLES) 111 109 112 72: 205 type=138 (ANGLES) 109 112 113 72: 206 type=138 (ANGLES) 109 112 114 72: 207 type=139 (ANGLES) 113 112 114 72: 208 type=122 (ANGLES) 104 115 116 72: 209 type=123 (ANGLES) 104 115 117 72: 210 type=124 (ANGLES) 116 115 117 72: 211 type=125 (ANGLES) 115 117 118 72: 212 type=126 (ANGLES) 115 117 119 72: 213 type=127 (ANGLES) 118 117 119 72: 214 type=116 (ANGLES) 117 119 120 72: 215 type=128 (ANGLES) 117 119 121 72: 216 type=129 (ANGLES) 117 119 134 72: 217 type=118 (ANGLES) 120 119 121 72: 218 type=116 (ANGLES) 120 119 134 72: 219 type=119 (ANGLES) 121 119 134 72: 220 type=118 (ANGLES) 119 121 122 72: 221 type=118 (ANGLES) 119 121 123 72: 222 type=120 (ANGLES) 119 121 124 72: 223 type=121 (ANGLES) 122 121 123 72: 224 type=118 (ANGLES) 122 121 124 72: 225 type=118 (ANGLES) 123 121 124 72: 226 type=118 (ANGLES) 121 124 125 72: 227 type=120 (ANGLES) 121 124 126 72: 228 type=120 (ANGLES) 121 124 130 72: 229 type=118 (ANGLES) 125 124 126 72: 230 type=118 (ANGLES) 125 124 130 72: 231 type=120 (ANGLES) 126 124 130 72: 232 type=118 (ANGLES) 124 126 127 72: 233 type=118 (ANGLES) 124 126 128 72: 234 type=118 (ANGLES) 124 126 129 72: 235 type=121 (ANGLES) 127 126 128 72: 236 type=121 (ANGLES) 127 126 129 72: 237 type=121 (ANGLES) 128 126 129 72: 238 type=118 (ANGLES) 124 130 131 72: 239 type=118 (ANGLES) 124 130 132 72: 240 type=118 (ANGLES) 124 130 133 72: 241 type=121 (ANGLES) 131 130 132 72: 242 type=121 (ANGLES) 131 130 133 72: 243 type=121 (ANGLES) 132 130 133 72: 244 type=122 (ANGLES) 119 134 135 72: 245 type=123 (ANGLES) 119 134 136 72: 246 type=124 (ANGLES) 135 134 136 72: 247 type=125 (ANGLES) 134 136 137 72: 248 type=126 (ANGLES) 134 136 138 72: 249 type=127 (ANGLES) 137 136 138 72: 250 type=116 (ANGLES) 136 138 139 72: 251 type=128 (ANGLES) 136 138 140 72: 252 type=129 (ANGLES) 136 138 144 72: 253 type=118 (ANGLES) 139 138 140 72: 254 type=116 (ANGLES) 139 138 144 72: 255 type=119 (ANGLES) 140 138 144 72: 256 type=118 (ANGLES) 138 140 141 72: 257 type=118 (ANGLES) 138 140 142 72: 258 type=118 (ANGLES) 138 140 143 72: 259 type=121 (ANGLES) 141 140 142 72: 260 type=121 (ANGLES) 141 140 143 72: 261 type=121 (ANGLES) 142 140 143 72: 262 type=122 (ANGLES) 138 144 145 72: 263 type=123 (ANGLES) 138 144 146 72: 264 type=124 (ANGLES) 145 144 146 72: 265 type=125 (ANGLES) 144 146 147 72: 266 type=126 (ANGLES) 144 146 148 72: 267 type=127 (ANGLES) 147 146 148 72: 268 type=116 (ANGLES) 146 148 149 72: 269 type=128 (ANGLES) 146 148 150 72: 270 type=129 (ANGLES) 146 148 154 72: 271 type=118 (ANGLES) 149 148 150 72: 272 type=116 (ANGLES) 149 148 154 72: 273 type=119 (ANGLES) 150 148 154 72: 274 type=118 (ANGLES) 148 150 151 72: 275 type=118 (ANGLES) 148 150 152 72: 276 type=118 (ANGLES) 148 150 153 72: 277 type=121 (ANGLES) 151 150 152 72: 278 type=121 (ANGLES) 151 150 153 72: 279 type=121 (ANGLES) 152 150 153 72: 280 type=122 (ANGLES) 148 154 155 72: G96Angle: 72: nr: 0 72: Restr. Angles: 72: nr: 0 72: Lin. Angle: 72: nr: 0 72: Bond-Cross: 72: nr: 0 72: BA-Cross: 72: nr: 0 72: U-B: 72: nr: 0 72: Quartic Angles: 72: nr: 0 72: Tab. Angles: 72: nr: 0 72: Proper Dih.: 72: nr: 145 72: iatoms: 72: 0 type=140 (PDIHS) 4 24 22 23 72: 1 type=141 (PDIHS) 22 26 24 25 72: 2 type=140 (PDIHS) 26 40 38 39 72: 3 type=141 (PDIHS) 38 42 40 41 72: 4 type=140 (PDIHS) 42 60 58 59 72: 5 type=142 (PDIHS) 44 47 50 48 72: 6 type=142 (PDIHS) 47 52 48 49 72: 7 type=142 (PDIHS) 47 54 50 51 72: 8 type=142 (PDIHS) 48 56 52 53 72: 9 type=142 (PDIHS) 50 56 54 55 72: 10 type=142 (PDIHS) 52 54 56 57 72: 11 type=141 (PDIHS) 58 62 60 61 72: 12 type=140 (PDIHS) 62 67 65 66 72: 13 type=141 (PDIHS) 65 69 67 68 72: 14 type=140 (PDIHS) 69 91 89 90 72: 15 type=141 (PDIHS) 77 82 80 81 72: 16 type=140 (PDIHS) 80 83 82 86 72: 17 type=141 (PDIHS) 82 84 83 85 72: 18 type=141 (PDIHS) 82 87 86 88 72: 19 type=141 (PDIHS) 89 93 91 92 72: 20 type=140 (PDIHS) 93 102 100 101 72: 21 type=141 (PDIHS) 100 104 102 103 72: 22 type=140 (PDIHS) 104 117 115 116 72: 23 type=140 (PDIHS) 109 113 112 114 72: 24 type=141 (PDIHS) 115 119 117 118 72: 25 type=140 (PDIHS) 119 136 134 135 72: 26 type=141 (PDIHS) 134 138 136 137 72: 27 type=140 (PDIHS) 138 146 144 145 72: 28 type=141 (PDIHS) 144 148 146 147 72: Ryckaert-Bell.: 72: nr: 1565 72: iatoms: 72: 0 type=143 (RBDIHS) 1 0 4 5 72: 1 type=144 (RBDIHS) 1 0 4 6 72: 2 type=144 (RBDIHS) 1 0 4 22 72: 3 type=143 (RBDIHS) 2 0 4 5 72: 4 type=144 (RBDIHS) 2 0 4 6 72: 5 type=144 (RBDIHS) 2 0 4 22 72: 6 type=143 (RBDIHS) 3 0 4 5 72: 7 type=144 (RBDIHS) 3 0 4 6 72: 8 type=144 (RBDIHS) 3 0 4 22 72: 9 type=145 (RBDIHS) 0 4 6 9 72: 10 type=146 (RBDIHS) 22 4 6 9 72: 11 type=147 (RBDIHS) 0 4 6 7 72: 12 type=147 (RBDIHS) 0 4 6 8 72: 13 type=148 (RBDIHS) 5 4 6 7 72: 14 type=148 (RBDIHS) 5 4 6 8 72: 15 type=148 (RBDIHS) 5 4 6 9 72: 16 type=149 (RBDIHS) 22 4 6 7 72: 17 type=149 (RBDIHS) 22 4 6 8 72: 18 type=150 (RBDIHS) 0 4 22 24 72: 19 type=151 (RBDIHS) 6 4 22 24 72: 20 type=148 (RBDIHS) 4 6 9 10 72: 21 type=148 (RBDIHS) 4 6 9 11 72: 22 type=152 (RBDIHS) 4 6 9 12 72: 23 type=148 (RBDIHS) 7 6 9 10 72: 24 type=148 (RBDIHS) 7 6 9 11 72: 25 type=148 (RBDIHS) 7 6 9 12 72: 26 type=148 (RBDIHS) 8 6 9 10 72: 27 type=148 (RBDIHS) 8 6 9 11 72: 28 type=148 (RBDIHS) 8 6 9 12 72: 29 type=148 (RBDIHS) 6 9 12 13 72: 30 type=148 (RBDIHS) 6 9 12 14 72: 31 type=152 (RBDIHS) 6 9 12 15 72: 32 type=148 (RBDIHS) 10 9 12 13 72: 33 type=148 (RBDIHS) 10 9 12 14 72: 34 type=148 (RBDIHS) 10 9 12 15 72: 35 type=148 (RBDIHS) 11 9 12 13 72: 36 type=148 (RBDIHS) 11 9 12 14 72: 37 type=148 (RBDIHS) 11 9 12 15 72: 38 type=148 (RBDIHS) 9 12 15 16 72: 39 type=148 (RBDIHS) 9 12 15 17 72: 40 type=153 (RBDIHS) 9 12 15 18 72: 41 type=148 (RBDIHS) 13 12 15 16 72: 42 type=148 (RBDIHS) 13 12 15 17 72: 43 type=154 (RBDIHS) 13 12 15 18 72: 44 type=148 (RBDIHS) 14 12 15 16 72: 45 type=148 (RBDIHS) 14 12 15 17 72: 46 type=154 (RBDIHS) 14 12 15 18 72: 47 type=144 (RBDIHS) 12 15 18 19 72: 48 type=144 (RBDIHS) 12 15 18 20 72: 49 type=144 (RBDIHS) 12 15 18 21 72: 50 type=143 (RBDIHS) 16 15 18 19 72: 51 type=143 (RBDIHS) 16 15 18 20 72: 52 type=143 (RBDIHS) 16 15 18 21 72: 53 type=143 (RBDIHS) 17 15 18 19 72: 54 type=143 (RBDIHS) 17 15 18 20 72: 55 type=143 (RBDIHS) 17 15 18 21 72: 56 type=155 (RBDIHS) 4 22 24 25 72: 57 type=156 (RBDIHS) 4 22 24 26 72: 58 type=155 (RBDIHS) 23 22 24 25 72: 59 type=157 (RBDIHS) 23 22 24 26 72: 60 type=158 (RBDIHS) 22 24 26 28 72: 61 type=159 (RBDIHS) 22 24 26 38 72: 62 type=160 (RBDIHS) 24 26 28 30 72: 63 type=160 (RBDIHS) 24 26 28 34 72: 64 type=161 (RBDIHS) 38 26 28 30 72: 65 type=161 (RBDIHS) 38 26 28 34 72: 66 type=147 (RBDIHS) 24 26 28 29 72: 67 type=148 (RBDIHS) 27 26 28 29 72: 68 type=148 (RBDIHS) 27 26 28 30 72: 69 type=148 (RBDIHS) 27 26 28 34 72: 70 type=149 (RBDIHS) 38 26 28 29 72: 71 type=150 (RBDIHS) 24 26 38 40 72: 72 type=151 (RBDIHS) 28 26 38 40 72: 73 type=148 (RBDIHS) 26 28 30 31 72: 74 type=148 (RBDIHS) 26 28 30 32 72: 75 type=148 (RBDIHS) 26 28 30 33 72: 76 type=148 (RBDIHS) 29 28 30 31 72: 77 type=148 (RBDIHS) 29 28 30 32 72: 78 type=148 (RBDIHS) 29 28 30 33 72: 79 type=148 (RBDIHS) 34 28 30 31 72: 80 type=148 (RBDIHS) 34 28 30 32 72: 81 type=148 (RBDIHS) 34 28 30 33 72: 82 type=148 (RBDIHS) 26 28 34 35 72: 83 type=148 (RBDIHS) 26 28 34 36 72: 84 type=148 (RBDIHS) 26 28 34 37 72: 85 type=148 (RBDIHS) 29 28 34 35 72: 86 type=148 (RBDIHS) 29 28 34 36 72: 87 type=148 (RBDIHS) 29 28 34 37 72: 88 type=148 (RBDIHS) 30 28 34 35 72: 89 type=148 (RBDIHS) 30 28 34 36 72: 90 type=148 (RBDIHS) 30 28 34 37 72: 91 type=155 (RBDIHS) 26 38 40 41 72: 92 type=156 (RBDIHS) 26 38 40 42 72: 93 type=155 (RBDIHS) 39 38 40 41 72: 94 type=157 (RBDIHS) 39 38 40 42 72: 95 type=158 (RBDIHS) 38 40 42 44 72: 96 type=159 (RBDIHS) 38 40 42 58 72: 97 type=147 (RBDIHS) 40 42 44 45 72: 98 type=147 (RBDIHS) 40 42 44 46 72: 99 type=162 (RBDIHS) 40 42 44 47 72: 100 type=148 (RBDIHS) 43 42 44 45 72: 101 type=148 (RBDIHS) 43 42 44 46 72: 102 type=163 (RBDIHS) 43 42 44 47 72: 103 type=149 (RBDIHS) 58 42 44 45 72: 104 type=149 (RBDIHS) 58 42 44 46 72: 105 type=164 (RBDIHS) 58 42 44 47 72: 106 type=150 (RBDIHS) 40 42 58 60 72: 107 type=151 (RBDIHS) 44 42 58 60 72: 108 type=165 (RBDIHS) 44 47 48 49 72: 109 type=165 (RBDIHS) 44 47 48 52 72: 110 type=165 (RBDIHS) 50 47 48 49 72: 111 type=165 (RBDIHS) 50 47 48 52 72: 112 type=165 (RBDIHS) 44 47 50 51 72: 113 type=165 (RBDIHS) 44 47 50 54 72: 114 type=165 (RBDIHS) 48 47 50 51 72: 115 type=165 (RBDIHS) 48 47 50 54 72: 116 type=165 (RBDIHS) 47 48 52 53 72: 117 type=165 (RBDIHS) 47 48 52 56 72: 118 type=165 (RBDIHS) 49 48 52 53 72: 119 type=165 (RBDIHS) 49 48 52 56 72: 120 type=165 (RBDIHS) 47 50 54 55 72: 121 type=165 (RBDIHS) 47 50 54 56 72: 122 type=165 (RBDIHS) 51 50 54 55 72: 123 type=165 (RBDIHS) 51 50 54 56 72: 124 type=165 (RBDIHS) 48 52 56 54 72: 125 type=165 (RBDIHS) 48 52 56 57 72: 126 type=165 (RBDIHS) 53 52 56 54 72: 127 type=165 (RBDIHS) 53 52 56 57 72: 128 type=165 (RBDIHS) 50 54 56 52 72: 129 type=165 (RBDIHS) 50 54 56 57 72: 130 type=165 (RBDIHS) 55 54 56 52 72: 131 type=165 (RBDIHS) 55 54 56 57 72: 132 type=155 (RBDIHS) 42 58 60 61 72: 133 type=156 (RBDIHS) 42 58 60 62 72: 134 type=155 (RBDIHS) 59 58 60 61 72: 135 type=157 (RBDIHS) 59 58 60 62 72: 136 type=159 (RBDIHS) 58 60 62 65 72: 137 type=150 (RBDIHS) 60 62 65 67 72: 138 type=155 (RBDIHS) 62 65 67 68 72: 139 type=156 (RBDIHS) 62 65 67 69 72: 140 type=155 (RBDIHS) 66 65 67 68 72: 141 type=157 (RBDIHS) 66 65 67 69 72: 142 type=158 (RBDIHS) 65 67 69 71 72: 143 type=159 (RBDIHS) 65 67 69 89 72: 144 type=166 (RBDIHS) 67 69 71 74 72: 145 type=167 (RBDIHS) 89 69 71 74 72: 146 type=147 (RBDIHS) 67 69 71 72 72: 147 type=147 (RBDIHS) 67 69 71 73 72: 148 type=148 (RBDIHS) 70 69 71 72 72: 149 type=148 (RBDIHS) 70 69 71 73 72: 150 type=148 (RBDIHS) 70 69 71 74 72: 151 type=149 (RBDIHS) 89 69 71 72 72: 152 type=149 (RBDIHS) 89 69 71 73 72: 153 type=150 (RBDIHS) 67 69 89 91 72: 154 type=151 (RBDIHS) 71 69 89 91 72: 155 type=148 (RBDIHS) 69 71 74 75 72: 156 type=148 (RBDIHS) 69 71 74 76 72: 157 type=152 (RBDIHS) 69 71 74 77 72: 158 type=148 (RBDIHS) 72 71 74 75 72: 159 type=148 (RBDIHS) 72 71 74 76 72: 160 type=148 (RBDIHS) 72 71 74 77 72: 161 type=148 (RBDIHS) 73 71 74 75 72: 162 type=148 (RBDIHS) 73 71 74 76 72: 163 type=148 (RBDIHS) 73 71 74 77 72: 164 type=148 (RBDIHS) 71 74 77 78 72: 165 type=148 (RBDIHS) 71 74 77 79 72: 166 type=153 (RBDIHS) 71 74 77 80 72: 167 type=148 (RBDIHS) 75 74 77 78 72: 168 type=148 (RBDIHS) 75 74 77 79 72: 169 type=168 (RBDIHS) 75 74 77 80 72: 170 type=148 (RBDIHS) 76 74 77 78 72: 171 type=148 (RBDIHS) 76 74 77 79 72: 172 type=168 (RBDIHS) 76 74 77 80 72: 173 type=169 (RBDIHS) 74 77 80 81 72: 174 type=170 (RBDIHS) 74 77 80 82 72: 175 type=171 (RBDIHS) 78 77 80 82 72: 176 type=171 (RBDIHS) 79 77 80 82 72: 177 type=172 (RBDIHS) 77 80 82 83 72: 178 type=172 (RBDIHS) 77 80 82 86 72: 179 type=173 (RBDIHS) 81 80 82 83 72: 180 type=173 (RBDIHS) 81 80 82 86 72: 181 type=173 (RBDIHS) 80 82 83 84 72: 182 type=173 (RBDIHS) 80 82 83 85 72: 183 type=173 (RBDIHS) 86 82 83 84 72: 184 type=173 (RBDIHS) 86 82 83 85 72: 185 type=173 (RBDIHS) 80 82 86 87 72: 186 type=173 (RBDIHS) 80 82 86 88 72: 187 type=173 (RBDIHS) 83 82 86 87 72: 188 type=173 (RBDIHS) 83 82 86 88 72: 189 type=155 (RBDIHS) 69 89 91 92 72: 190 type=156 (RBDIHS) 69 89 91 93 72: 191 type=155 (RBDIHS) 90 89 91 92 72: 192 type=157 (RBDIHS) 90 89 91 93 72: 193 type=158 (RBDIHS) 89 91 93 95 72: 194 type=159 (RBDIHS) 89 91 93 100 72: 195 type=174 (RBDIHS) 91 93 95 98 72: 196 type=175 (RBDIHS) 100 93 95 98 72: 197 type=147 (RBDIHS) 91 93 95 96 72: 198 type=147 (RBDIHS) 91 93 95 97 72: 199 type=148 (RBDIHS) 94 93 95 96 72: 200 type=148 (RBDIHS) 94 93 95 97 72: 201 type=176 (RBDIHS) 94 93 95 98 72: 202 type=149 (RBDIHS) 100 93 95 96 72: 203 type=149 (RBDIHS) 100 93 95 97 72: 204 type=150 (RBDIHS) 91 93 100 102 72: 205 type=151 (RBDIHS) 95 93 100 102 72: 206 type=177 (RBDIHS) 93 95 98 99 72: 207 type=178 (RBDIHS) 96 95 98 99 72: 208 type=178 (RBDIHS) 97 95 98 99 72: 209 type=155 (RBDIHS) 93 100 102 103 72: 210 type=156 (RBDIHS) 93 100 102 104 72: 211 type=155 (RBDIHS) 101 100 102 103 72: 212 type=157 (RBDIHS) 101 100 102 104 72: 213 type=158 (RBDIHS) 100 102 104 106 72: 214 type=159 (RBDIHS) 100 102 104 115 72: 215 type=179 (RBDIHS) 102 104 106 109 72: 216 type=180 (RBDIHS) 115 104 106 109 72: 217 type=147 (RBDIHS) 102 104 106 107 72: 218 type=147 (RBDIHS) 102 104 106 108 72: 219 type=148 (RBDIHS) 105 104 106 107 72: 220 type=148 (RBDIHS) 105 104 106 108 72: 221 type=148 (RBDIHS) 105 104 106 109 72: 222 type=149 (RBDIHS) 115 104 106 107 72: 223 type=149 (RBDIHS) 115 104 106 108 72: 224 type=150 (RBDIHS) 102 104 115 117 72: 225 type=151 (RBDIHS) 106 104 115 117 72: 226 type=148 (RBDIHS) 104 106 109 110 72: 227 type=148 (RBDIHS) 104 106 109 111 72: 228 type=181 (RBDIHS) 104 106 109 112 72: 229 type=148 (RBDIHS) 107 106 109 110 72: 230 type=148 (RBDIHS) 107 106 109 111 72: 231 type=182 (RBDIHS) 107 106 109 112 72: 232 type=148 (RBDIHS) 108 106 109 110 72: 233 type=148 (RBDIHS) 108 106 109 111 72: 234 type=182 (RBDIHS) 108 106 109 112 72: 235 type=183 (RBDIHS) 106 109 112 113 72: 236 type=183 (RBDIHS) 106 109 112 114 72: 237 type=155 (RBDIHS) 104 115 117 118 72: 238 type=156 (RBDIHS) 104 115 117 119 72: 239 type=155 (RBDIHS) 116 115 117 118 72: 240 type=157 (RBDIHS) 116 115 117 119 72: 241 type=158 (RBDIHS) 115 117 119 121 72: 242 type=159 (RBDIHS) 115 117 119 134 72: 243 type=184 (RBDIHS) 117 119 121 124 72: 244 type=185 (RBDIHS) 134 119 121 124 72: 245 type=147 (RBDIHS) 117 119 121 122 72: 246 type=147 (RBDIHS) 117 119 121 123 72: 247 type=148 (RBDIHS) 120 119 121 122 72: 248 type=148 (RBDIHS) 120 119 121 123 72: 249 type=148 (RBDIHS) 120 119 121 124 72: 250 type=149 (RBDIHS) 134 119 121 122 72: 251 type=149 (RBDIHS) 134 119 121 123 72: 252 type=150 (RBDIHS) 117 119 134 136 72: 253 type=151 (RBDIHS) 121 119 134 136 72: 254 type=148 (RBDIHS) 119 121 124 125 72: 255 type=152 (RBDIHS) 119 121 124 126 72: 256 type=152 (RBDIHS) 119 121 124 130 72: 257 type=148 (RBDIHS) 122 121 124 125 72: 258 type=148 (RBDIHS) 122 121 124 126 72: 259 type=148 (RBDIHS) 122 121 124 130 72: 260 type=148 (RBDIHS) 123 121 124 125 72: 261 type=148 (RBDIHS) 123 121 124 126 72: 262 type=148 (RBDIHS) 123 121 124 130 72: 263 type=148 (RBDIHS) 121 124 126 127 72: 264 type=148 (RBDIHS) 121 124 126 128 72: 265 type=148 (RBDIHS) 121 124 126 129 72: 266 type=148 (RBDIHS) 125 124 126 127 72: 267 type=148 (RBDIHS) 125 124 126 128 72: 268 type=148 (RBDIHS) 125 124 126 129 72: 269 type=148 (RBDIHS) 130 124 126 127 72: 270 type=148 (RBDIHS) 130 124 126 128 72: 271 type=148 (RBDIHS) 130 124 126 129 72: 272 type=148 (RBDIHS) 121 124 130 131 72: 273 type=148 (RBDIHS) 121 124 130 132 72: 274 type=148 (RBDIHS) 121 124 130 133 72: 275 type=148 (RBDIHS) 125 124 130 131 72: 276 type=148 (RBDIHS) 125 124 130 132 72: 277 type=148 (RBDIHS) 125 124 130 133 72: 278 type=148 (RBDIHS) 126 124 130 131 72: 279 type=148 (RBDIHS) 126 124 130 132 72: 280 type=148 (RBDIHS) 126 124 130 133 72: 281 type=155 (RBDIHS) 119 134 136 137 72: 282 type=156 (RBDIHS) 119 134 136 138 72: 283 type=155 (RBDIHS) 135 134 136 137 72: 284 type=157 (RBDIHS) 135 134 136 138 72: 285 type=158 (RBDIHS) 134 136 138 140 72: 286 type=159 (RBDIHS) 134 136 138 144 72: 287 type=147 (RBDIHS) 136 138 140 141 72: 288 type=147 (RBDIHS) 136 138 140 142 72: 289 type=147 (RBDIHS) 136 138 140 143 72: 290 type=148 (RBDIHS) 139 138 140 141 72: 291 type=148 (RBDIHS) 139 138 140 142 72: 292 type=148 (RBDIHS) 139 138 140 143 72: 293 type=149 (RBDIHS) 144 138 140 141 72: 294 type=149 (RBDIHS) 144 138 140 142 72: 295 type=149 (RBDIHS) 144 138 140 143 72: 296 type=150 (RBDIHS) 136 138 144 146 72: 297 type=151 (RBDIHS) 140 138 144 146 72: 298 type=155 (RBDIHS) 138 144 146 147 72: 299 type=156 (RBDIHS) 138 144 146 148 72: 300 type=155 (RBDIHS) 145 144 146 147 72: 301 type=157 (RBDIHS) 145 144 146 148 72: 302 type=158 (RBDIHS) 144 146 148 150 72: 303 type=159 (RBDIHS) 144 146 148 154 72: 304 type=147 (RBDIHS) 146 148 150 151 72: 305 type=147 (RBDIHS) 146 148 150 152 72: 306 type=147 (RBDIHS) 146 148 150 153 72: 307 type=148 (RBDIHS) 149 148 150 151 72: 308 type=148 (RBDIHS) 149 148 150 152 72: 309 type=148 (RBDIHS) 149 148 150 153 72: 310 type=149 (RBDIHS) 154 148 150 151 72: 311 type=149 (RBDIHS) 154 148 150 152 72: 312 type=149 (RBDIHS) 154 148 150 153 72: Restr. Dih.: 72: nr: 0 72: CBT Dih.: 72: nr: 0 72: Fourier Dih.: 72: nr: 0 72: Improper Dih.: 72: nr: 0 72: Per. Imp. Dih.: 72: nr: 0 72: Tab. Dih.: 72: nr: 0 72: CMAP Dih.: 72: nr: 0 72: GB 1-2 Pol.: 72: nr: 0 72: GB 1-3 Pol.: 72: nr: 0 72: GB 1-4 Pol.: 72: nr: 0 72: GB Polariz.: 72: nr: 0 72: Nonpolar Sol.: 72: nr: 0 72: LJ-14: 72: nr: 1197 72: iatoms: 72: 0 type=186 (LJ14) 0 7 72: 1 type=186 (LJ14) 0 8 72: 2 type=187 (LJ14) 0 9 72: 3 type=188 (LJ14) 0 23 72: 4 type=189 (LJ14) 0 24 72: 5 type=190 (LJ14) 1 5 72: 6 type=190 (LJ14) 1 6 72: 7 type=190 (LJ14) 1 22 72: 8 type=190 (LJ14) 2 5 72: 9 type=190 (LJ14) 2 6 72: 10 type=190 (LJ14) 2 22 72: 11 type=190 (LJ14) 3 5 72: 12 type=190 (LJ14) 3 6 72: 13 type=190 (LJ14) 3 22 72: 14 type=191 (LJ14) 4 10 72: 15 type=191 (LJ14) 4 11 72: 16 type=192 (LJ14) 4 12 72: 17 type=190 (LJ14) 4 25 72: 18 type=192 (LJ14) 4 26 72: 19 type=193 (LJ14) 5 7 72: 20 type=193 (LJ14) 5 8 72: 21 type=191 (LJ14) 5 9 72: 22 type=194 (LJ14) 5 23 72: 23 type=186 (LJ14) 5 24 72: 24 type=191 (LJ14) 6 13 72: 25 type=191 (LJ14) 6 14 72: 26 type=192 (LJ14) 6 15 72: 27 type=195 (LJ14) 6 23 72: 28 type=187 (LJ14) 6 24 72: 29 type=193 (LJ14) 7 10 72: 30 type=193 (LJ14) 7 11 72: 31 type=191 (LJ14) 7 12 72: 32 type=196 (LJ14) 7 22 72: 33 type=193 (LJ14) 8 10 72: 34 type=193 (LJ14) 8 11 72: 35 type=191 (LJ14) 8 12 72: 36 type=196 (LJ14) 8 22 72: 37 type=191 (LJ14) 9 16 72: 38 type=191 (LJ14) 9 17 72: 39 type=187 (LJ14) 9 18 72: 40 type=197 (LJ14) 9 22 72: 41 type=193 (LJ14) 10 13 72: 42 type=193 (LJ14) 10 14 72: 43 type=191 (LJ14) 10 15 72: 44 type=193 (LJ14) 11 13 72: 45 type=193 (LJ14) 11 14 72: 46 type=191 (LJ14) 11 15 72: 47 type=190 (LJ14) 12 19 72: 48 type=190 (LJ14) 12 20 72: 49 type=190 (LJ14) 12 21 72: 50 type=193 (LJ14) 13 16 72: 51 type=193 (LJ14) 13 17 72: 52 type=186 (LJ14) 13 18 72: 53 type=193 (LJ14) 14 16 72: 54 type=193 (LJ14) 14 17 72: 55 type=186 (LJ14) 14 18 72: 56 type=190 (LJ14) 16 19 72: 57 type=190 (LJ14) 16 20 72: 58 type=190 (LJ14) 16 21 72: 59 type=190 (LJ14) 17 19 72: 60 type=190 (LJ14) 17 20 72: 61 type=190 (LJ14) 17 21 72: 62 type=196 (LJ14) 22 27 72: 63 type=197 (LJ14) 22 28 72: 64 type=198 (LJ14) 22 38 72: 65 type=190 (LJ14) 23 25 72: 66 type=195 (LJ14) 23 26 72: 67 type=186 (LJ14) 24 29 72: 68 type=187 (LJ14) 24 30 72: 69 type=187 (LJ14) 24 34 72: 70 type=188 (LJ14) 24 39 72: 71 type=189 (LJ14) 24 40 72: 72 type=190 (LJ14) 25 27 72: 73 type=190 (LJ14) 25 28 72: 74 type=190 (LJ14) 25 38 72: 75 type=191 (LJ14) 26 31 72: 76 type=191 (LJ14) 26 32 72: 77 type=191 (LJ14) 26 33 72: 78 type=191 (LJ14) 26 35 72: 79 type=191 (LJ14) 26 36 72: 80 type=191 (LJ14) 26 37 72: 81 type=190 (LJ14) 26 41 72: 82 type=192 (LJ14) 26 42 72: 83 type=193 (LJ14) 27 29 72: 84 type=191 (LJ14) 27 30 72: 85 type=191 (LJ14) 27 34 72: 86 type=194 (LJ14) 27 39 72: 87 type=186 (LJ14) 27 40 72: 88 type=195 (LJ14) 28 39 72: 89 type=187 (LJ14) 28 40 72: 90 type=193 (LJ14) 29 31 72: 91 type=193 (LJ14) 29 32 72: 92 type=193 (LJ14) 29 33 72: 93 type=193 (LJ14) 29 35 72: 94 type=193 (LJ14) 29 36 72: 95 type=193 (LJ14) 29 37 72: 96 type=196 (LJ14) 29 38 72: 97 type=191 (LJ14) 30 35 72: 98 type=191 (LJ14) 30 36 72: 99 type=191 (LJ14) 30 37 72: 100 type=197 (LJ14) 30 38 72: 101 type=191 (LJ14) 31 34 72: 102 type=191 (LJ14) 32 34 72: 103 type=191 (LJ14) 33 34 72: 104 type=197 (LJ14) 34 38 72: 105 type=196 (LJ14) 38 43 72: 106 type=197 (LJ14) 38 44 72: 107 type=198 (LJ14) 38 58 72: 108 type=190 (LJ14) 39 41 72: 109 type=195 (LJ14) 39 42 72: 110 type=186 (LJ14) 40 45 72: 111 type=186 (LJ14) 40 46 72: 112 type=199 (LJ14) 40 47 72: 113 type=188 (LJ14) 40 59 72: 114 type=189 (LJ14) 40 60 72: 115 type=190 (LJ14) 41 43 72: 116 type=190 (LJ14) 41 44 72: 117 type=190 (LJ14) 41 58 72: 118 type=200 (LJ14) 42 48 72: 119 type=200 (LJ14) 42 50 72: 120 type=190 (LJ14) 42 61 72: 121 type=192 (LJ14) 42 62 72: 122 type=193 (LJ14) 43 45 72: 123 type=193 (LJ14) 43 46 72: 124 type=201 (LJ14) 43 47 72: 125 type=194 (LJ14) 43 59 72: 126 type=186 (LJ14) 43 60 72: 127 type=202 (LJ14) 44 49 72: 128 type=202 (LJ14) 44 51 72: 129 type=200 (LJ14) 44 52 72: 130 type=200 (LJ14) 44 54 72: 131 type=195 (LJ14) 44 59 72: 132 type=187 (LJ14) 44 60 72: 133 type=201 (LJ14) 45 48 72: 134 type=201 (LJ14) 45 50 72: 135 type=196 (LJ14) 45 58 72: 136 type=201 (LJ14) 46 48 72: 137 type=201 (LJ14) 46 50 72: 138 type=196 (LJ14) 46 58 72: 139 type=203 (LJ14) 47 53 72: 140 type=203 (LJ14) 47 55 72: 141 type=204 (LJ14) 47 56 72: 142 type=205 (LJ14) 47 58 72: 143 type=203 (LJ14) 48 51 72: 144 type=204 (LJ14) 48 54 72: 145 type=203 (LJ14) 48 57 72: 146 type=203 (LJ14) 49 50 72: 147 type=206 (LJ14) 49 53 72: 148 type=203 (LJ14) 49 56 72: 149 type=204 (LJ14) 50 52 72: 150 type=203 (LJ14) 50 57 72: 151 type=206 (LJ14) 51 55 72: 152 type=203 (LJ14) 51 56 72: 153 type=203 (LJ14) 52 55 72: 154 type=203 (LJ14) 53 54 72: 155 type=206 (LJ14) 53 57 72: 156 type=206 (LJ14) 55 57 72: 157 type=196 (LJ14) 58 63 72: 158 type=196 (LJ14) 58 64 72: 159 type=198 (LJ14) 58 65 72: 160 type=190 (LJ14) 59 61 72: 161 type=195 (LJ14) 59 62 72: 162 type=188 (LJ14) 60 66 72: 163 type=189 (LJ14) 60 67 72: 164 type=190 (LJ14) 61 63 72: 165 type=190 (LJ14) 61 64 72: 166 type=190 (LJ14) 61 65 72: 167 type=190 (LJ14) 62 68 72: 168 type=192 (LJ14) 62 69 72: 169 type=194 (LJ14) 63 66 72: 170 type=186 (LJ14) 63 67 72: 171 type=194 (LJ14) 64 66 72: 172 type=186 (LJ14) 64 67 72: 173 type=196 (LJ14) 65 70 72: 174 type=197 (LJ14) 65 71 72: 175 type=198 (LJ14) 65 89 72: 176 type=190 (LJ14) 66 68 72: 177 type=195 (LJ14) 66 69 72: 178 type=186 (LJ14) 67 72 72: 179 type=186 (LJ14) 67 73 72: 180 type=187 (LJ14) 67 74 72: 181 type=188 (LJ14) 67 90 72: 182 type=189 (LJ14) 67 91 72: 183 type=190 (LJ14) 68 70 72: 184 type=190 (LJ14) 68 71 72: 185 type=190 (LJ14) 68 89 72: 186 type=191 (LJ14) 69 75 72: 187 type=191 (LJ14) 69 76 72: 188 type=192 (LJ14) 69 77 72: 189 type=190 (LJ14) 69 92 72: 190 type=192 (LJ14) 69 93 72: 191 type=193 (LJ14) 70 72 72: 192 type=193 (LJ14) 70 73 72: 193 type=191 (LJ14) 70 74 72: 194 type=194 (LJ14) 70 90 72: 195 type=186 (LJ14) 70 91 72: 196 type=191 (LJ14) 71 78 72: 197 type=191 (LJ14) 71 79 72: 198 type=187 (LJ14) 71 80 72: 199 type=195 (LJ14) 71 90 72: 200 type=187 (LJ14) 71 91 72: 201 type=193 (LJ14) 72 75 72: 202 type=193 (LJ14) 72 76 72: 203 type=191 (LJ14) 72 77 72: 204 type=196 (LJ14) 72 89 72: 205 type=193 (LJ14) 73 75 72: 206 type=193 (LJ14) 73 76 72: 207 type=191 (LJ14) 73 77 72: 208 type=196 (LJ14) 73 89 72: 209 type=190 (LJ14) 74 81 72: 210 type=207 (LJ14) 74 82 72: 211 type=197 (LJ14) 74 89 72: 212 type=193 (LJ14) 75 78 72: 213 type=193 (LJ14) 75 79 72: 214 type=186 (LJ14) 75 80 72: 215 type=193 (LJ14) 76 78 72: 216 type=193 (LJ14) 76 79 72: 217 type=186 (LJ14) 76 80 72: 218 type=187 (LJ14) 77 83 72: 219 type=187 (LJ14) 77 86 72: 220 type=190 (LJ14) 78 81 72: 221 type=208 (LJ14) 78 82 72: 222 type=190 (LJ14) 79 81 72: 223 type=208 (LJ14) 79 82 72: 224 type=190 (LJ14) 80 84 72: 225 type=190 (LJ14) 80 85 72: 226 type=190 (LJ14) 80 87 72: 227 type=190 (LJ14) 80 88 72: 228 type=190 (LJ14) 81 83 72: 229 type=190 (LJ14) 81 86 72: 230 type=190 (LJ14) 83 87 72: 231 type=190 (LJ14) 83 88 72: 232 type=190 (LJ14) 84 86 72: 233 type=190 (LJ14) 85 86 72: 234 type=196 (LJ14) 89 94 72: 235 type=197 (LJ14) 89 95 72: 236 type=198 (LJ14) 89 100 72: 237 type=190 (LJ14) 90 92 72: 238 type=195 (LJ14) 90 93 72: 239 type=186 (LJ14) 91 96 72: 240 type=186 (LJ14) 91 97 72: 241 type=209 (LJ14) 91 98 72: 242 type=188 (LJ14) 91 101 72: 243 type=189 (LJ14) 91 102 72: 244 type=190 (LJ14) 92 94 72: 245 type=190 (LJ14) 92 95 72: 246 type=190 (LJ14) 92 100 72: 247 type=190 (LJ14) 93 99 72: 248 type=190 (LJ14) 93 103 72: 249 type=192 (LJ14) 93 104 72: 250 type=193 (LJ14) 94 96 72: 251 type=193 (LJ14) 94 97 72: 252 type=210 (LJ14) 94 98 72: 253 type=194 (LJ14) 94 101 72: 254 type=186 (LJ14) 94 102 72: 255 type=195 (LJ14) 95 101 72: 256 type=187 (LJ14) 95 102 72: 257 type=190 (LJ14) 96 99 72: 258 type=196 (LJ14) 96 100 72: 259 type=190 (LJ14) 97 99 72: 260 type=196 (LJ14) 97 100 72: 261 type=211 (LJ14) 98 100 72: 262 type=196 (LJ14) 100 105 72: 263 type=197 (LJ14) 100 106 72: 264 type=198 (LJ14) 100 115 72: 265 type=190 (LJ14) 101 103 72: 266 type=195 (LJ14) 101 104 72: 267 type=186 (LJ14) 102 107 72: 268 type=186 (LJ14) 102 108 72: 269 type=187 (LJ14) 102 109 72: 270 type=188 (LJ14) 102 116 72: 271 type=189 (LJ14) 102 117 72: 272 type=190 (LJ14) 103 105 72: 273 type=190 (LJ14) 103 106 72: 274 type=190 (LJ14) 103 115 72: 275 type=191 (LJ14) 104 110 72: 276 type=191 (LJ14) 104 111 72: 277 type=197 (LJ14) 104 112 72: 278 type=190 (LJ14) 104 118 72: 279 type=192 (LJ14) 104 119 72: 280 type=193 (LJ14) 105 107 72: 281 type=193 (LJ14) 105 108 72: 282 type=191 (LJ14) 105 109 72: 283 type=194 (LJ14) 105 116 72: 284 type=186 (LJ14) 105 117 72: 285 type=195 (LJ14) 106 113 72: 286 type=195 (LJ14) 106 114 72: 287 type=195 (LJ14) 106 116 72: 288 type=187 (LJ14) 106 117 72: 289 type=193 (LJ14) 107 110 72: 290 type=193 (LJ14) 107 111 72: 291 type=196 (LJ14) 107 112 72: 292 type=196 (LJ14) 107 115 72: 293 type=193 (LJ14) 108 110 72: 294 type=193 (LJ14) 108 111 72: 295 type=196 (LJ14) 108 112 72: 296 type=196 (LJ14) 108 115 72: 297 type=197 (LJ14) 109 115 72: 298 type=194 (LJ14) 110 113 72: 299 type=194 (LJ14) 110 114 72: 300 type=194 (LJ14) 111 113 72: 301 type=194 (LJ14) 111 114 72: 302 type=196 (LJ14) 115 120 72: 303 type=197 (LJ14) 115 121 72: 304 type=198 (LJ14) 115 134 72: 305 type=190 (LJ14) 116 118 72: 306 type=195 (LJ14) 116 119 72: 307 type=186 (LJ14) 117 122 72: 308 type=186 (LJ14) 117 123 72: 309 type=187 (LJ14) 117 124 72: 310 type=188 (LJ14) 117 135 72: 311 type=189 (LJ14) 117 136 72: 312 type=190 (LJ14) 118 120 72: 313 type=190 (LJ14) 118 121 72: 314 type=190 (LJ14) 118 134 72: 315 type=191 (LJ14) 119 125 72: 316 type=192 (LJ14) 119 126 72: 317 type=192 (LJ14) 119 130 72: 318 type=190 (LJ14) 119 137 72: 319 type=192 (LJ14) 119 138 72: 320 type=193 (LJ14) 120 122 72: 321 type=193 (LJ14) 120 123 72: 322 type=191 (LJ14) 120 124 72: 323 type=194 (LJ14) 120 135 72: 324 type=186 (LJ14) 120 136 72: 325 type=191 (LJ14) 121 127 72: 326 type=191 (LJ14) 121 128 72: 327 type=191 (LJ14) 121 129 72: 328 type=191 (LJ14) 121 131 72: 329 type=191 (LJ14) 121 132 72: 330 type=191 (LJ14) 121 133 72: 331 type=195 (LJ14) 121 135 72: 332 type=187 (LJ14) 121 136 72: 333 type=193 (LJ14) 122 125 72: 334 type=191 (LJ14) 122 126 72: 335 type=191 (LJ14) 122 130 72: 336 type=196 (LJ14) 122 134 72: 337 type=193 (LJ14) 123 125 72: 338 type=191 (LJ14) 123 126 72: 339 type=191 (LJ14) 123 130 72: 340 type=196 (LJ14) 123 134 72: 341 type=197 (LJ14) 124 134 72: 342 type=193 (LJ14) 125 127 72: 343 type=193 (LJ14) 125 128 72: 344 type=193 (LJ14) 125 129 72: 345 type=193 (LJ14) 125 131 72: 346 type=193 (LJ14) 125 132 72: 347 type=193 (LJ14) 125 133 72: 348 type=191 (LJ14) 126 131 72: 349 type=191 (LJ14) 126 132 72: 350 type=191 (LJ14) 126 133 72: 351 type=191 (LJ14) 127 130 72: 352 type=191 (LJ14) 128 130 72: 353 type=191 (LJ14) 129 130 72: 354 type=196 (LJ14) 134 139 72: 355 type=197 (LJ14) 134 140 72: 356 type=198 (LJ14) 134 144 72: 357 type=190 (LJ14) 135 137 72: 358 type=195 (LJ14) 135 138 72: 359 type=186 (LJ14) 136 141 72: 360 type=186 (LJ14) 136 142 72: 361 type=186 (LJ14) 136 143 72: 362 type=188 (LJ14) 136 145 72: 363 type=189 (LJ14) 136 146 72: 364 type=190 (LJ14) 137 139 72: 365 type=190 (LJ14) 137 140 72: 366 type=190 (LJ14) 137 144 72: 367 type=190 (LJ14) 138 147 72: 368 type=192 (LJ14) 138 148 72: 369 type=193 (LJ14) 139 141 72: 370 type=193 (LJ14) 139 142 72: 371 type=193 (LJ14) 139 143 72: 372 type=194 (LJ14) 139 145 72: 373 type=186 (LJ14) 139 146 72: 374 type=195 (LJ14) 140 145 72: 375 type=187 (LJ14) 140 146 72: 376 type=196 (LJ14) 141 144 72: 377 type=196 (LJ14) 142 144 72: 378 type=196 (LJ14) 143 144 72: 379 type=196 (LJ14) 144 149 72: 380 type=197 (LJ14) 144 150 72: 381 type=198 (LJ14) 144 154 72: 382 type=190 (LJ14) 145 147 72: 383 type=195 (LJ14) 145 148 72: 384 type=186 (LJ14) 146 151 72: 385 type=186 (LJ14) 146 152 72: 386 type=186 (LJ14) 146 153 72: 387 type=188 (LJ14) 146 155 72: 388 type=190 (LJ14) 147 149 72: 389 type=190 (LJ14) 147 150 72: 390 type=190 (LJ14) 147 154 72: 391 type=193 (LJ14) 149 151 72: 392 type=193 (LJ14) 149 152 72: 393 type=193 (LJ14) 149 153 72: 394 type=194 (LJ14) 149 155 72: 395 type=195 (LJ14) 150 155 72: 396 type=196 (LJ14) 151 154 72: 397 type=196 (LJ14) 152 154 72: 398 type=196 (LJ14) 153 154 72: Coulomb-14: 72: nr: 0 72: LJC-14 q: 72: nr: 0 72: LJC Pairs NB: 72: nr: 0 72: LJ (SR): 72: nr: 0 72: Buck.ham (SR): 72: nr: 0 72: LJ: 72: nr: 0 72: B.ham: 72: nr: 0 72: Disper. corr.: 72: nr: 0 72: Coulomb (SR): 72: nr: 0 72: Coul: 72: nr: 0 72: RF excl.: 72: nr: 0 72: Coul. recip.: 72: nr: 0 72: LJ recip.: 72: nr: 0 72: DPD: 72: nr: 0 72: Polarization: 72: nr: 0 72: Water Pol.: 72: nr: 0 72: Thole Pol.: 72: nr: 0 72: Anharm. Pol.: 72: nr: 0 72: Position Rest.: 72: nr: 0 72: Flat-b. P-R.: 72: nr: 0 72: Dis. Rest.: 72: nr: 0 72: D.R.Viol. (nm): 72: nr: 0 72: Orient. Rest.: 72: nr: 0 72: Ori. R. RMSD: 72: nr: 0 72: Angle Rest.: 72: nr: 0 72: Angle Rest. Z: 72: nr: 0 72: Dih. Rest.: 72: nr: 0 72: Dih. Rest. Vi.: 72: nr: 0 72: Constraint: 72: nr: 0 72: Constr. No Co.: 72: nr: 0 72: Settle: 72: nr: 0 72: Virtual site 1: 72: nr: 0 72: Virtual site 2: 72: nr: 0 72: Virt. site 2fd: 72: nr: 0 72: Virtual site 3: 72: nr: 0 72: Virt. site 3fd: 72: nr: 0 72: Vir. site 3fad: 72: nr: 0 72: Vir. site 3out: 72: nr: 0 72: Virt. site 4fd: 72: nr: 0 72: Vir. site 4fdn: 72: nr: 0 72: Virtual site N: 72: nr: 0 72: COM Pull En.: 72: nr: 0 72: Dens. fitting: 72: nr: 0 72: Quantum En.: 72: nr: 0 72: NN Potential: 72: nr: 0 72: Potential: 72: nr: 0 72: Kinetic En.: 72: nr: 0 72: Total Energy: 72: nr: 0 72: Conserved En.: 72: nr: 0 72: Temperature: 72: nr: 0 72: Vir. Temp.: 72: nr: 0 72: Pres. DC: 72: nr: 0 72: Pressure: 72: nr: 0 72: dH/dl constr.: 72: nr: 0 72: dVremain/dl: 72: nr: 0 72: dEkin/dl: 72: nr: 0 72: dVcoul/dl: 72: nr: 0 72: dVvdw/dl: 72: nr: 0 72: dVbonded/dl: 72: nr: 0 72: dVrestraint/dl: 72: nr: 0 72: dVtemp/dl: 72: nr: 0 72: grp[T-Coupling ] nr=1, name=[ rest] 72: grp[Energy Mon. ] nr=1, name=[ rest] 72: grp[Acc. not used] nr=1, name=[ rest] 72: grp[Freeze ] nr=1, name=[ rest] 72: grp[User1 ] nr=1, name=[ rest] 72: grp[User2 ] nr=1, name=[ rest] 72: grp[VCM ] nr=1, name=[ rest] 72: grp[Compressed X] nr=1, name=[ rest] 72: grp[Or. Res. Fit] nr=1, name=[ rest] 72: grp[QMMM ] nr=1, name=[ rest] 72: grpname (11): 72: grpname[0]={name="System"} 72: grpname[1]={name="Protein"} 72: grpname[2]={name="Protein-H"} 72: grpname[3]={name="C-alpha"} 72: grpname[4]={name="Backbone"} 72: grpname[5]={name="MainChain"} 72: grpname[6]={name="MainChain+Cb"} 72: grpname[7]={name="MainChain+H"} 72: grpname[8]={name="SideChain"} 72: grpname[9]={name="SideChain-H"} 72: grpname[10]={name="rest"} 72: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 72: allocated 0 0 0 0 0 0 0 0 0 0 72: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 72: box (3x3): 72: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 72: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 72: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 72: box_rel (3x3): 72: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv (3x3): 72: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev (3x3): 72: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev (3x3): 72: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev (3x3): 72: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: nosehoover_xi: not available 72: x (156x3): 72: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 72: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 72: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 72: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 72: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 72: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 72: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 72: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 72: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 72: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 72: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 72: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 72: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 72: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 72: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 72: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 72: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 72: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 72: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 72: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 72: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 72: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 72: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 72: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 72: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 72: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 72: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 72: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 72: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 72: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 72: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 72: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 72: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 72: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 72: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 72: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 72: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 72: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 72: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 72: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 72: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 72: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 72: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 72: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 72: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 72: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 72: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 72: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 72: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 72: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 72: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 72: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 72: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 72: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 72: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 72: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 72: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 72: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 72: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 72: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 72: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 72: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 72: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 72: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 72: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 72: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 72: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 72: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 72: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 72: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 72: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 72: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 72: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 72: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 72: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 72: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 72: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 72: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 72: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 72: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 72: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 72: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 72: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 72: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 72: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 72: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 72: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 72: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 72: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 72: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 72: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 72: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 72: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 72: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 72: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 72: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 72: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 72: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 72: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 72: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 72: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 72: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 72: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 72: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 72: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 72: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 72: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 72: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 72: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 72: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 72: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 72: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 72: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 72: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 72: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 72: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 72: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 72: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 72: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 72: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 72: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 72: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 72: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 72: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 72: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 72: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 72: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 72: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 72: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 72: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 72: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 72: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 72: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 72: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 72: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 72: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 72: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 72: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 72: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 72: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 72: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 72: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 72: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 72: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 72: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 72: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 72: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 72: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 72: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 72: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 72: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 72: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 72: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 72: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 72: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 72: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 72: v (156x3): 72: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: Group statistics 72: T-Coupling : 156 (total 156 atoms) 72: Energy Mon. : 156 (total 156 atoms) 72: Acc. not used: 156 (total 156 atoms) 72: Freeze : 156 (total 156 atoms) 72: User1 : 156 (total 156 atoms) 72: User2 : 156 (total 156 atoms) 72: VCM : 156 (total 156 atoms) 72: Compressed X: 156 (total 156 atoms) 72: Or. Res. Fit: 156 (total 156 atoms) 72: QMMM : 156 (total 156 atoms) 72: [ OK ] DumpTest.WorksWithTpr (5 ms) 72: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: [ OK ] DumpTest.WorksWithTprAndMdpWriting (5 ms) 72: [----------] 2 tests from DumpTest (12 ms total) 72: 72: [----------] 3 tests from HelpwritingTest 72: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 72: [ OK ] HelpwritingTest.ConvertTprWritesHelp (3 ms) 72: [ RUN ] HelpwritingTest.DumpWritesHelp 72: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 72: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 72: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms) 72: [----------] 3 tests from HelpwritingTest (5 ms total) 72: 72: [----------] 7 tests from GmxMakeNdx 72: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 16 Protein residues 72: Analysing Protein... 72: 72: 0 System : 256 atoms 72: 1 Protein : 256 atoms 72: 2 Protein-H : 139 atoms 72: 3 C-alpha : 16 atoms 72: 4 Backbone : 48 atoms 72: 5 MainChain : 63 atoms 72: 6 MainChain+Cb : 78 atoms 72: 7 MainChain+H : 81 atoms 72: 8 SideChain : 175 atoms 72: 9 SideChain-H : 76 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (2 ms) 72: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 1 'Protein' 72: Copied index group 2 'Protein-H' 72: Merged two groups with OR: 22 10 -> 22 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNoStructureInput (4 ms) 72: [ RUN ] GmxMakeNdx.HandlesNotProtein 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNotProtein (1 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 4 'Backbone' 72: Copied index group 8 'SideChain' 72: Merged two groups with AND: 5 13 -> 0 72: Group is empty 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (1 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Removed group 0 'System' 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 72: [ RUN ] GmxMakeNdx.Splitres 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into residues 72: 72: > 72: [ OK ] GmxMakeNdx.Splitres (1 ms) 72: [ RUN ] GmxMakeNdx.Splitat 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into atoms 72: 72: > 72: [ OK ] GmxMakeNdx.Splitat (1 ms) 72: [----------] 7 tests from GmxMakeNdx (14 ms total) 72: 72: [----------] 4 tests from ReportMethodsTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -231825537 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectInformation 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 72: [ RUN ] ReportMethodsTest.ToolEndToEndTest 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: section: Methods 72: subsection: Simulation system 72: A system of 1 molecules (156 atoms) was simulated. 72: 72: subsection: Simulation settings 72: A total of 0 ns were simulated with a time step of 1 fs. 72: Neighbor searching was performed every 10 steps. 72: The Cut-off algorithm was used for electrostatic interactions. 72: with a cut-off of 1 nm. 72: A single cut-off of 1.1 nm was used for Van der Waals interactions. 72: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 72: [----------] 4 tests from ReportMethodsTest (1 ms total) 72: 72: [----------] 4 tests from ConvertTprTest 72: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Setting the LD random seed to -151955499 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 200000 72: Runtime for the run 200 ps 72: Run end step 200000 72: Run end time 200 ps 72: 72: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (235 ms) 72: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Setting the LD random seed to -623280789 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime to 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (234 ms) 72: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Setting nsteps to 102 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Setting the LD random seed to -1896433929 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 102 72: Runtime for the run 0.102 ps 72: Run end step 102 72: Run end time 0.102 ps 72: 72: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (231 ms) 72: [ RUN ] ConvertTprTest.generateVelocitiesTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Setting the LD random seed to 1772018687 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprTest.generateVelocitiesTest (233 ms) 72: [----------] 4 tests from ConvertTprTest (936 ms total) 72: 72: [----------] 1 test from ConvertTprNoVelocityTest 72: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: 72: NOTE 3 [file lysozyme.top, line 1465]: 72: Zero-step energy minimization will alter the coordinates before 72: calculating the energy. If you just want the energy of a single point, 72: try zero-step MD (with unconstrained_start = yes). To do multiple 72: single-point energy evaluations of different configurations of the same 72: topology, use mdrun -rerun. 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 72: Setting the LD random seed to -855171 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (208 ms) 72: [----------] 1 test from ConvertTprNoVelocityTest (208 ms total) 72: 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: trr version: GMX_trn_file (single precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:86: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (6 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:123: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md (0 ms) 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats (13 ms total) 72: 72: [----------] 35 tests from Works/TrjconvDumpTest 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (10 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (1 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (7 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (1 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (1 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 (0 ms) 72: [----------] 35 tests from Works/TrjconvDumpTest (32 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 70 tests from 8 test suites ran. (1726 ms total) 72: [ PASSED ] 63 tests. 72: [ SKIPPED ] 7 tests, listed below: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72/104 Test #72: ToolUnitTests ............................. Passed 1.74 sec test 73 Start 73: ToolWithLeaksUnitTests 73: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests 73: Test timeout computed to be: 1920 73: [==========] Running 2 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 1 test from ConvertTprTest 73: [ RUN ] ConvertTprTest.selectIndexTest 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2026.3-Debian_1 (single precision) 73: Setting the LD random seed to -17498433 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprTest.selectIndexTest (210 ms) 73: [----------] 1 test from ConvertTprTest (210 ms total) 73: 73: [----------] 1 test from ConvertTprNoVelocityTest 73: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: 73: NOTE 3 [file lysozyme.top, line 1465]: 73: Zero-step energy minimization will alter the coordinates before 73: calculating the energy. If you just want the energy of a single point, 73: try zero-step MD (with unconstrained_start = yes). To do multiple 73: single-point energy evaluations of different configurations of the same 73: topology, use mdrun -rerun. 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.3-Debian_1 (single precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2026.3-Debian_1 (single precision) 73: Setting the LD random seed to 2012478767 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (156 ms) 73: [----------] 1 test from ConvertTprNoVelocityTest (157 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 2 tests from 2 test suites ran. (368 ms total) 73: [ PASSED ] 2 tests. 73/104 Test #73: ToolWithLeaksUnitTests .................... Passed 0.39 sec test 74 Start 74: H5mdTests 74: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/h5md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/H5mdTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/h5md/tests 74: Test timeout computed to be: 60 74: [==========] Running 1 test from 1 test suite. 74: [----------] Global test environment set-up. 74: [----------] 1 test from H5mdDisabledTest 74: [ RUN ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled 74: [ OK ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled (0 ms) 74: [----------] 1 test from H5mdDisabledTest (0 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 1 test from 1 test suite ran. (0 ms total) 74: [ PASSED ] 1 test. 74/104 Test #74: H5mdTests ................................. Passed 0.02 sec test 75 Start 75: FileIOTests 75: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/FileIOTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/fileio/tests 75: Test timeout computed to be: 60 75: [==========] Running 432 tests from 17 test suites. 75: [----------] Global test environment set-up. 75: [----------] 4 tests from Checkpoint 75: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 75: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 75: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 75: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripInt64 75: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripReal 75: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 75: [----------] 4 tests from Checkpoint (0 ms total) 75: 75: [----------] 1 test from StructureIOTest 75: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 75: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 75: [----------] 1 test from StructureIOTest (0 ms total) 75: 75: [----------] 2 tests from FileMD5Test 75: [ RUN ] FileMD5Test.CanComputeMD5 75: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 75: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 75: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 75: [----------] 2 tests from FileMD5Test (1 ms total) 75: 75: [----------] 4 tests from FileTypeTest 75: [ RUN ] FileTypeTest.CorrectValueForEmptyString 75: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForNoExtension 75: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 75: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 75: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 75: [----------] 4 tests from FileTypeTest (0 ms total) 75: 75: [----------] 4 tests from ColorMapTest 75: [ RUN ] ColorMapTest.CanReadFromFile 75: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 75: [ RUN ] ColorMapTest.CanWriteToFile 75: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 75: [ RUN ] ColorMapTest.RoundTrip 75: [ OK ] ColorMapTest.RoundTrip (0 ms) 75: [ RUN ] ColorMapTest.SearchWorks 75: [ OK ] ColorMapTest.SearchWorks (0 ms) 75: [----------] 4 tests from ColorMapTest (0 ms total) 75: 75: [----------] 4 tests from MatioTest 75: [ RUN ] MatioTest.CanWriteToFile 75: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 75: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanConvertToNewRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 75: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) 75: [----------] 4 tests from MatioTest (1 ms total) 75: 75: [----------] 3 tests from MrcSerializer 75: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 75: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 75: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 75: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 75: [----------] 3 tests from MrcSerializer (0 ms total) 75: 75: [----------] 4 tests from MrcDensityMap 75: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 75: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 75: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 75: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 75: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 75: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 75: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 75: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 75: [----------] 4 tests from MrcDensityMap (1 ms total) 75: 75: [----------] 8 tests from MrcDensityMapHeaderTest 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 75: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.IsSane 75: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 75: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 75: 75: [----------] 10 tests from ReadTest 75: [ RUN ] ReadTest.get_eint_ReadsInteger 75: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_eint64_ReadsInteger 75: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsInteger 75: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsFloat 75: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 75: [ RUN ] ReadTest.get_ereal_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not a 75: real value 75: 75: 75: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 75: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 75: [----------] 10 tests from ReadTest (0 ms total) 75: 75: [----------] 3 tests from TimeControlTest 75: [ RUN ] TimeControlTest.UnSetHasNoValue 75: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 75: [ RUN ] TimeControlTest.CanSetValue 75: [ OK ] TimeControlTest.CanSetValue (0 ms) 75: [ RUN ] TimeControlTest.CanUnsetValueAgain 75: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 75: [----------] 3 tests from TimeControlTest (0 ms total) 75: 75: [----------] 1 test from TngTest 75: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 75: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 75: [----------] 1 test from TngTest (0 ms total) 75: 75: [----------] 4 tests from XvgioTest 75: [ RUN ] XvgioTest.readXvgIntWorks 75: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgRealWorks 75: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 75: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgDeprecatedWorks 75: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 75: [----------] 4 tests from XvgioTest (0 ms total) 75: 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 75: 75: [----------] 370 tests from FileTypeMatch/FileTypeTest 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 (0 ms) 75: [----------] 370 tests from FileTypeMatch/FileTypeTest (1 ms total) 75: 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 (0 ms) 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 (0 ms) 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest (0 ms total) 75: 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (2 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (5 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 432 tests from 17 test suites ran. (15 ms total) 75: [ PASSED ] 432 tests. 75/104 Test #75: FileIOTests ............................... Passed 0.04 sec test 76 Start 76: SelectionUnitTests 76: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/SelectionUnitTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/gromacs/selection/tests 76: Test timeout computed to be: 60 76: [==========] Running 202 tests from 11 test suites. 76: [----------] Global test environment set-up. 76: [----------] 1 test from IndexGroupTest 76: [ RUN ] IndexGroupTest.RemovesDuplicates 76: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 76: [----------] 1 test from IndexGroupTest (0 ms total) 76: 76: [----------] 15 tests from IndexBlockTest 76: [ RUN ] IndexBlockTest.CreatesUnknownBlock 76: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms) 76: [ RUN ] IndexBlockTest.CreatesAtomBlock 76: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesSingleBlock 76: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 76: [----------] 15 tests from IndexBlockTest (4 ms total) 76: 76: [----------] 11 tests from IndexMapTest 76: [ RUN ] IndexMapTest.InitializesAtomBlock 76: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 76: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 76: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 76: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 76: [ RUN ] IndexMapTest.InitializesMoleculeBlock 76: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsSingleBlock 76: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocks 76: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 76: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 76: [ RUN ] IndexMapTest.HandlesMultipleRequests 76: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 76: [----------] 11 tests from IndexMapTest (5 ms total) 76: 76: [----------] 3 tests from IndexGroupsAndNamesTest 76: [ RUN ] IndexGroupsAndNamesTest.containsNames 76: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 76: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 76: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 76: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 76: 76: [----------] 15 tests from NeighborhoodSearchTest 76: [ RUN ] NeighborhoodSearchTest.SimpleSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSearch (8 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 76: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (8 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchBox 76: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 76: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 76: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 76: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 76: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (21 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 76: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 76: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 76: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 76: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 76: [----------] 15 tests from NeighborhoodSearchTest (53 ms total) 76: 76: [----------] 13 tests from PositionCalculationTest 76: [ RUN ] PositionCalculationTest.ComputesAtomPositions 76: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 76: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionMask 76: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 76: [----------] 13 tests from PositionCalculationTest (7 ms total) 76: 76: [----------] 33 tests from SelectionCollectionTest 76: [ RUN ] SelectionCollectionTest.HandlesNoSelections 76: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 76: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 76: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 76: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 76: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 76: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 76: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 76: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 76: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 76: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 76: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 76: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 76: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 76: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 76: [----------] 33 tests from SelectionCollectionTest (10 ms total) 76: 76: [----------] 14 tests from SelectionCollectionInteractiveTest 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 76: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 76: [----------] 14 tests from SelectionCollectionInteractiveTest (12 ms total) 76: 76: [----------] 71 tests from SelectionCollectionDataTest 76: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 76: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 76: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResnr 76: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 76: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 76: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 76: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesChain 76: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMass 76: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCharge 76: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 76: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 76: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 76: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBeta 76: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResname 76: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 76: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 76: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 76: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 76: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 76: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 76: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 76: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 76: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 76: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 76: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 76: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (1 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 76: [----------] 71 tests from SelectionCollectionDataTest (80 ms total) 76: 76: [----------] 17 tests from SelectionOptionTest 76: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 76: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 76: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 76: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 76: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptySelections 76: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 76: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelections 76: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 76: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesAdjuster 76: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 76: [----------] 17 tests from SelectionOptionTest (3 ms total) 76: 76: [----------] 9 tests from SelectionFileOptionTest 76: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 76: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 76: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 76: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 202 tests from 11 test suites ran. (180 ms total) 76: [ PASSED ] 202 tests. 76/104 Test #76: SelectionUnitTests ........................ Passed 0.20 sec test 77 Start 77: MdrunOutputTests 77: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunOutputTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 12 tests from 5 test suites. 77: [----------] Global test environment set-up. 77: [----------] 1 test from MdrunTest 77: [ RUN ] MdrunTest.WritesHelp 77: [ OK ] MdrunTest.WritesHelp (20 ms) 77: [----------] 1 test from MdrunTest (20 ms total) 77: 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to 1866326015 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.024 0.012 198.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 14.397 1.667 6.001 0.001 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (36 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -4194454 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 197.4 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 29.382 0.817 2.941 0.002 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (19 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -338231413 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.008 197.4 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 22.213 1.080 3.890 0.002 77: Reading frame 0 time 0.000 77: # Atoms 3 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (22 ms) 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (78 ms total) 77: 77: [----------] 2 tests from Argon12/OutputFiles 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.152 0.076 199.9 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 19.321 1.242 4.472 0.003 77: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (97 ms) 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.073 0.037 199.7 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 39.935 0.601 2.163 0.006 77: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (47 ms) 77: [----------] 2 tests from Argon12/OutputFiles (144 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/Trajectories 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -741475602 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.028 0.014 198.7 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 43.053 0.557 2.007 0.003 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (30 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -1835841 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.008 197.8 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 79.834 0.301 1.082 0.006 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (28 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -16785442 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.006 196.5 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 103.917 0.231 0.831 0.007 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (20 ms) 77: [----------] 3 tests from MdrunCanWrite/Trajectories (79 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -620888065 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.008 0.004 196.5 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 66.177 0.363 1.306 0.005 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (17 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 77: 77: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: The Berendsen barostat does not generate any strictly correct ensemble, 77: and should not be used for new production simulations (in our opinion). 77: We recommend using the C-rescale barostat instead. 77: 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: 77: There was 1 WARNING 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -38821891 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 195.9 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 67.736 0.354 1.276 0.005 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (13 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2026.3-Debian_1 (single precision) 77: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -1613799457 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.016 0.008 197.8 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 32.060 0.749 2.695 0.002 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (18 ms) 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories (50 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 12 tests from 5 test suites ran. (435 ms total) 77: [ PASSED ] 12 tests. 77/104 Test #77: MdrunOutputTests .......................... Passed 0.46 sec test 78 Start 78: MdrunModulesTests 78: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunModulesTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 15 tests from 3 test suites. 78: [----------] Global test environment set-up. 78: [----------] 9 tests from DensityFittingTest 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.8565254e+03 78: Maximum force = 4.5099883e+03 on atom 3 78: Norm of force = 1.6816849e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1111491625 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (15 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -9.8207725e+03 78: Maximum force = 7.3954834e+03 on atom 2 78: Norm of force = 2.7825089e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1241515274 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (13 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (11 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Overriding nsteps with value passed on the command line: 4 steps 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 4 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 5 steps. 78: Potential Energy = -5.4739321e+03 78: Maximum force = 6.1322017e+03 on atom 2 78: Norm of force = 1.7702150e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 1996351231 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (13 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (11 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.8565254e+03 78: Maximum force = 4.5099883e+03 on atom 3 78: Norm of force = 1.6816849e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1090619201 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (13 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -2.7138664e+04 78: Maximum force = 6.7827656e+03 on atom 2 78: Norm of force = 1.9608866e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1749033041 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (12 ms) 78: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: Setting the LD random seed to -1079257194 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 78: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (11 ms) 78: [ RUN ] DensityFittingTest.CheckpointWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (2) 78: 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -90345241 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.018 0.009 198.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 27.971 0.858 3.089 0.004 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 78: Can not increase nstlist because an NVE ensemble is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: NOTE: 23 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.070 0.035 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 12.275 1.955 7.039 0.002 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (65 ms) 78: [----------] 9 tests from DensityFittingTest (170 ms total) 78: 78: [----------] 4 tests from MimicTest 78: [ RUN ] MimicTest.OneQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 58 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.011 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 8.075 2.972 10.700 0.001 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1114703048 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.OneQuantumMol (27 ms) 78: [ RUN ] MimicTest.AllQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.002 0.001 191.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 77.816 0.308 1.110 0.011 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2108608439 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.AllQuantumMol (21 ms) 78: [ RUN ] MimicTest.TwoQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 16 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.000 183.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 259.404 0.093 0.333 0.036 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1184577154 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.TwoQuantumMol (15 ms) 78: [ RUN ] MimicTest.BondCuts 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 66.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: NVE simulation: will use the initial temperature of 300.368 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 78: 78: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 11 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.001 190.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 109.682 0.219 0.788 0.029 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -570557441 78: 78: Generated 2211 of the 2211 non-bonded parameter combinations 78: 78: Generated 2211 of the 2211 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.BondCuts (27 ms) 78: [----------] 4 tests from MimicTest (91 ms total) 78: 78: [----------] 2 tests from WithIntegrator/ImdTest 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 78: Generating 1-4 interactions: fudge = 1 78: 78: NOTE 1 [file glycine_vacuo.top, line 12]: 78: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 78: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 78: the time step of 2.0e-03 ps. 78: Maybe you forgot to change the constraints mdp option. 78: 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 55519. 78: IMD: -imdwait not set, starting simulation. 78: starting mdrun 'Glycine' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -558934 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: NOTE: 15 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.045 0.023 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 22.961 1.045 7.526 0.001 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (126 ms) 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 78: apply to steep. 78: 78: Generating 1-4 interactions: fudge = 1 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2026.3-Debian_1 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 38055. 78: IMD: -imdwait not set, starting simulation. 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = 1.1977065e+03 78: Maximum force = 1.7794877e+04 on atom 9 78: Norm of force = 7.8732901e+03 78: Setting the LD random seed to -1828782642 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (57 ms) 78: [----------] 2 tests from WithIntegrator/ImdTest (183 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 15 tests from 3 test suites ran. (492 ms total) 78: [ PASSED ] 15 tests. 78/104 Test #78: MdrunModulesTests ......................... Passed 0.52 sec test 79 Start 79: MdrunIOTests 79: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunIOTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 76 tests from 13 test suites. 79: [----------] Global test environment set-up. 79: [----------] 9 tests from GromppTest 79: [ RUN ] GromppTest.EmptyMdpFileWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -436346913 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.EmptyMdpFileWorks (7 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group rest: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -427009 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorks (4 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group Methanol: Single, 3 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 3.0 280.0 79: 6.0- 270.0 79: Simulated annealing for group SOL: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group Methanol is 7.20 79: Number of degrees of freedom in T-Coupling group SOL is 4.80 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to 1962925983 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (6 ms) 79: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 79: Setting the LD random seed to -121782785 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (11 ms) 79: [ RUN ] GromppTest.HandlesMaxwarn 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: The Berendsen thermostat does not generate the correct kinetic energy 79: distribution, and should not be used for new production simulations (in 79: our opinion). We would recommend the V-rescale thermostat. 79: 79: Number of degrees of freedom in T-Coupling group System is 12.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Setting the LD random seed to -656482345 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.HandlesMaxwarn (5 ms) 79: [ RUN ] GromppTest.MaxwarnShouldBePositive 79: [ OK ] GromppTest.MaxwarnShouldBePositive (1 ms) 79: [ RUN ] GromppTest.ValidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: 0.613 nm 0.000 nm 79: 79: There were 3 NOTEs 79: Setting the LD random seed to 872320975 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.ValidTransformationCoord (7 ms) 79: [ RUN ] GromppTest.InvalidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: Setting the LD random seed to 2130702283 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: [ OK ] GromppTest.InvalidTransformationCoord (6 ms) 79: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 79: Setting the LD random seed to 2141712767 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (10 ms) 79: [----------] 9 tests from GromppTest (62 ms total) 79: 79: [----------] 6 tests from MdrunTerminationTest 79: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to 794721199 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 27.195 0.883 3.177 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 43 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.019 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 13.486 1.780 6.406 0.001 79: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (51 ms) 79: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 1.032 to 1 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 79: Setting the LD random seed to -1375896881 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 15.856 1.514 5.449 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 102 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 100 79: Runtime for the run 0.1 ps 79: Run end step 100 79: Run end time 0.1 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 102 79: Runtime for the run 0.102 ps 79: Run end step 102 79: Run end time 0.102 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 37 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.020 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 435.727 0.055 0.198 0.030 79: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (60 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to 921645043 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 49 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 24.232 0.990 3.565 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 21 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.048 0.024 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.782 2.226 8.013 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 6 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 63.629 0.377 1.358 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 8 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 8 79: Runtime for the run 0.008 ps 79: Run end step 8 79: Run end time 0.008 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 60.284 0.398 1.433 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: NOTE: 23 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.000 170.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 578.894 0.041 0.149 0.040 79: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (79 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -1216422017 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 48.392 0.496 1.785 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 52.587 0.456 1.643 0.004 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (25 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -1681990914 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 64.268 0.373 1.344 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 4 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (10 ms) 79: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -135876979 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.007 0.004 197.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 71.458 0.336 1.209 0.005 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.007 0.004 198.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 71.397 0.336 1.210 0.005 79: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (16 ms) 79: [----------] 6 tests from MdrunTerminationTest (246 ms total) 79: 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 352.437 0.068 0.245 0.024 79: trr version: GMX_trn_file (single precision) 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: 79: Dumping frame at t= 0.016 ps 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Last frame -1 time 0.016 79: 79: There were 3 NOTEs 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: Analysing residue names: 79: There are: 2 Water residues 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: Reading Coordinates, Velocities and Box size from old trajectory 79: 79: Will read whole trajectory 79: 79: Using frame at t = 0.016 ps 79: 79: Starting time for run is 0 ps 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (15 ms) 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 10 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.151 0.075 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.488 1.232 4.434 0.001 79: 79: 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (82 ms) 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (98 ms total) 79: 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.011 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 128.225 0.187 0.674 0.018 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 197.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 134.069 0.179 0.644 0.019 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 154.970 0.155 0.558 0.022 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (58 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 293.473 0.082 0.294 0.041 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 161.492 0.149 0.535 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 197.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 175.179 0.137 0.493 0.024 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (39 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 286.499 0.084 0.302 0.040 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 176.402 0.136 0.490 0.025 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 163.960 0.146 0.527 0.023 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (35 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 289.352 0.083 0.299 0.040 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 164.299 0.146 0.526 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 165.634 0.145 0.522 0.023 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (33 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 282.804 0.085 0.306 0.039 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 186.563 0.129 0.463 0.026 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 189.964 0.126 0.455 0.026 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (30 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 338.345 0.071 0.255 0.047 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 196.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 198.159 0.121 0.436 0.028 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 175.566 0.137 0.492 0.024 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (28 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 332.520 0.072 0.260 0.046 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 179.538 0.134 0.481 0.025 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 191.380 0.125 0.451 0.027 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (28 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 292.762 0.082 0.295 0.041 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 196.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 197.726 0.121 0.437 0.027 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 187.248 0.128 0.461 0.026 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (28 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 203.253 0.118 0.425 0.014 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.054 0.028 196.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 28.256 0.849 3.058 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 197.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 129.240 0.186 0.669 0.009 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (64 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.011 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 127.755 0.188 0.676 0.009 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.208 0.255 0.917 0.007 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 19 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.016 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 49.577 0.484 1.743 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (65 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 312.705 0.077 0.276 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 131.073 0.183 0.659 0.009 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 94.495 0.254 0.914 0.007 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (32 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 306.971 0.078 0.281 0.021 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 192.237 0.125 0.449 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 164.847 0.146 0.524 0.011 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (27 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 331.786 0.072 0.260 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 193.022 0.124 0.448 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 183.912 0.130 0.470 0.013 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (26 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 356.660 0.067 0.242 0.025 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 200.732 0.120 0.430 0.014 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 195.322 0.123 0.442 0.014 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (26 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 385.109 0.062 0.224 0.027 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 196.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 202.678 0.118 0.426 0.014 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 192.237 0.125 0.449 0.013 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (24 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 363.221 0.066 0.238 0.025 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 180.612 0.133 0.478 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 156.584 0.153 0.552 0.011 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (26 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 236.727 0.101 0.365 0.079 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.013 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 59.398 0.404 1.455 0.020 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 196.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 113.772 0.211 0.759 0.038 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (58 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.019 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.723 0.313 1.126 0.026 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 196.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 119.346 0.201 0.724 0.040 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 196.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 125.611 0.191 0.688 0.042 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (132 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 182.758 0.131 0.473 0.061 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.048 0.024 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 32.394 0.741 2.667 0.011 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 196.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 124.589 0.193 0.693 0.042 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (91 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 171.949 0.140 0.502 0.058 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 64.365 0.373 1.342 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 136.813 0.175 0.632 0.046 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (79 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 256.254 0.094 0.337 0.086 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 143.249 0.168 0.603 0.048 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 152.427 0.157 0.567 0.051 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (60 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 241.195 0.100 0.358 0.081 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 18 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.037 0.018 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 42.365 0.567 2.039 0.014 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 159.175 0.151 0.543 0.053 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (145 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.044 0.022 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 67.169 0.357 1.286 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 148.243 0.162 0.583 0.050 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 154.734 0.155 0.558 0.052 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (73 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.043 0.022 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 67.802 0.354 1.274 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.056 0.028 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 27.874 0.861 3.100 0.009 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.622 0.227 0.818 0.035 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (147 ms) 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1366 ms total) 79: 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 154.591 0.155 0.559 0.064 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.078 0.039 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.908 1.206 4.340 0.008 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 196.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.114 0.231 0.830 0.043 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (97 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.010 189.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 151.247 0.159 0.571 0.063 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 195.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 87.222 0.275 0.991 0.036 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 197.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 92.443 0.260 0.935 0.039 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (92 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 35 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.058 0.029 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 50.504 0.475 1.711 0.021 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 85.606 0.280 1.009 0.036 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 80.509 0.298 1.073 0.034 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (106 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 32 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.057 0.028 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 51.839 0.463 1.667 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 89.890 0.267 0.961 0.037 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 194.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 100.175 0.240 0.862 0.042 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (99 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.627 0.314 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 4.681 5.127 18.458 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.821 0.431 190.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 1.806 13.291 47.849 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.661 0.330 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 2.353 10.198 36.713 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (1182 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.109 0.055 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 26.790 0.896 3.225 0.011 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 80.930 0.297 1.068 0.034 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.013 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 57.728 0.416 1.497 0.024 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (295 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 124.404 0.193 0.695 0.052 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 195.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 109.837 0.219 0.787 0.046 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 89.806 0.267 0.962 0.037 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (101 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.015 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.426 0.252 0.905 0.040 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 26 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 196.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 74.891 0.320 1.154 0.031 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.019 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 39.908 0.601 2.165 0.017 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (130 ms) 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2105 ms total) 79: 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.018 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 82.844 0.290 1.043 0.012 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 195.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 139.083 0.173 0.621 0.019 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 197.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 118.703 0.202 0.728 0.016 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (59 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.171 0.086 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 17.133 1.401 5.043 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.055 0.027 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 28.314 0.848 3.052 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.013 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 57.754 0.416 1.496 0.008 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (160 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 234.216 0.102 0.369 0.033 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.060 0.030 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 25.822 0.929 3.346 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.012 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 62.727 0.383 1.377 0.009 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (69 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 302.553 0.079 0.286 0.042 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 196.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 184.672 0.130 0.468 0.026 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 182.584 0.131 0.473 0.025 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (29 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.004 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 327.587 0.073 0.264 0.045 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 194.669 0.123 0.444 0.027 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.543 0.271 200.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 2.866 8.375 30.152 0.000 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (292 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.425 0.213 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.903 3.477 12.517 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.248 0.124 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.264 3.832 13.794 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.080 0.040 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.360 1.240 4.463 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (495 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 165.607 0.145 0.522 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 136.721 0.176 0.632 0.019 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 197.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 100.710 0.238 0.858 0.014 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (53 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 243.309 0.099 0.355 0.034 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 196.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.335 0.224 0.805 0.015 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 197.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 88.411 0.271 0.977 0.012 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (51 ms) 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1211 ms total) 79: 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 191.162 0.126 0.452 0.027 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 196.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 118.501 0.203 0.729 0.016 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 152.899 0.157 0.565 0.021 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (42 ms) 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 288.525 0.083 0.299 0.040 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 146.026 0.164 0.592 0.020 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 146.736 0.164 0.589 0.020 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (38 ms) 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (80 ms total) 79: 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 168.015 0.143 0.514 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 96.772 0.248 0.893 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 63.314 0.379 1.365 0.009 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (47 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 314.060 0.076 0.275 0.044 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 148.162 0.162 0.583 0.021 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 171.929 0.140 0.503 0.024 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (38 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 210.547 0.114 0.410 0.029 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 196.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 163.393 0.147 0.529 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 198.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 132.689 0.181 0.651 0.018 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (36 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 197.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 316.659 0.076 0.273 0.044 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 22 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.075 0.037 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 20.809 1.153 4.152 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 158.256 0.152 0.546 0.022 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (63 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 246.060 0.098 0.351 0.034 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 145.259 0.165 0.595 0.020 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 25 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.075 0.038 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 20.637 1.163 4.187 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (70 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 309.655 0.078 0.279 0.043 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 146.301 0.164 0.591 0.020 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 197.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 130.397 0.184 0.663 0.018 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (31 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 236.946 0.101 0.365 0.033 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 146.380 0.164 0.590 0.020 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 148.777 0.161 0.581 0.021 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (33 ms) 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (321 ms total) 79: 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 79: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 17 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.042 0.021 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 69.188 0.347 1.249 0.010 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.066 0.033 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 23.434 1.024 3.687 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.006 197.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 138.228 0.174 0.625 0.019 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (81 ms) 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (81 ms total) 79: 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.080 0.040 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 36.575 0.656 2.362 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.042 0.021 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 37.200 0.645 2.323 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.080 0.040 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.444 1.234 4.444 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (126 ms) 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 181.135 0.132 0.477 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 112.056 0.214 0.771 0.008 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 57 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.018 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 43.430 0.553 1.989 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (53 ms) 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (181 ms total) 79: 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Setting the AWH bias MC random seed to -34357524 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -4756481 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 197.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 160.876 0.149 0.537 0.041 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 196.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 81.263 0.295 1.063 0.021 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 196.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 80.860 0.297 1.069 0.021 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (93 ms) 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: Setting the AWH bias MC random seed to -1610776582 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -306188561 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 187.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 121.436 0.198 0.711 0.031 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.013 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 60.069 0.400 1.438 0.015 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 196.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 86.427 0.278 1.000 0.022 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (103 ms) 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (197 ms total) 79: 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 79: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 21 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.046 0.023 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 63.649 0.377 1.357 0.027 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 20 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.044 0.022 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 35.513 0.676 2.433 0.015 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 197.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.178 0.230 0.829 0.043 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (115 ms) 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (115 ms total) 79: 79: [----------] 3 tests from Checking/InitialConstraintsTest 79: [ RUN ] Checking/InitialConstraintsTest.Works/0 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to 1073151830 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.004 197.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 43.011 0.558 2.009 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (11 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/1 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to -9015593 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.007 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 25.472 0.942 3.392 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (12 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: Integrator method md-vv-avek is implemented primarily for validation 79: purposes; for molecular dynamics, you should probably be using md or 79: md-vv 79: 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2026.3-Debian_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to -88603 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.007 0.003 196.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 50.276 0.477 1.719 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (11 ms) 79: [----------] 3 tests from Checking/InitialConstraintsTest (36 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 76 tests from 13 test suites ran. (6254 ms total) 79: [ PASSED ] 76 tests. 79/104 Test #79: MdrunIOTests .............................. Passed 6.28 sec test 80 Start 80: MdrunTestsOneRank 80: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 31 tests from 9 test suites. 80: [----------] Global test environment set-up. 80: [----------] 2 tests from AwhTest 80: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.184 0.092 199.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 19.713 1.217 4.383 0.005 80: [ OK ] AwhTest.SingleBiasMultiDimCanRun (114 ms) 80: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.028 199.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 64.301 0.373 1.344 0.016 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: NOTE: 13 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.022 199.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 81.014 0.296 1.066 0.021 80: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (81 ms) 80: [----------] 2 tests from AwhTest (196 ms total) 80: 80: [----------] 1 test from CompelTest 80: [ RUN ] CompelTest.SwapCanRun 80: Generating 1-4 interactions: fudge = 0.5 80: Split0 group 'Ch0' contains 83 atoms. 80: Split1 group 'Ch1' contains 83 atoms. 80: Solvent group 'SOL' contains 11931 atoms. 80: Swap group 'NA+' contains 19 atoms. 80: Swap group 'CL-' contains 19 atoms. 80: Number of degrees of freedom in T-Coupling group System is 27869.00 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Determining initial numbers of ions per compartment. 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 2 steps, 0.0 ps. 80: Setting the LD random seed to 805173903 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning all bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.183 0.092 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 11.315 2.121 30.545 0.452 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 80: 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Copying channel fluxes from checkpoint file data 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: NOTE: 21 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.161 0.081 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 12.837 1.870 26.922 0.513 80: [ OK ] CompelTest.SwapCanRun (446 ms) 80: [----------] 1 test from CompelTest (446 ms total) 80: 80: [----------] 6 tests from BondedInteractionsTest 80: [ RUN ] BondedInteractionsTest.NormalBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 51 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 199.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 11.255 2.132 7.677 0.001 80: Setting the LD random seed to -1157660705 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalBondWorks (16 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 51 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 12.078 1.987 7.153 0.001 80: Setting the LD random seed to -621428741 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedBondWorks (17 ms) 80: [ RUN ] BondedInteractionsTest.NormalAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 53 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 12.281 1.954 7.035 0.001 80: Setting the LD random seed to -945346821 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalAngleWorks (16 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 52 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.011 0.005 198.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 16.096 1.491 5.368 0.001 80: Setting the LD random seed to -67 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (14 ms) 80: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 16 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 184.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 381.060 0.063 0.227 0.018 80: Setting the LD random seed to 2063582846 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalDihedralWorks (5 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.000 189.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 173.891 0.138 0.497 0.008 80: Setting the LD random seed to -1157719297 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (7 ms) 80: [----------] 6 tests from BondedInteractionsTest (79 ms total) 80: 80: [----------] 2 tests from BoxDeformationTest 80: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 25 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 164.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1035.394 0.023 0.167 0.072 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1073742338 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Setting gen_seed to -1094721667 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (6 ms) 80: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group rest is 1293.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 20 steps, 0.0 ps. 80: Setting the LD random seed to 1543466940 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 80: 80: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 80: 80: Estimate for the relative computational load of the PME mesh part: 0.23 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.168 0.084 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 43.139 0.556 4.006 0.162 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2566 ms) 80: [----------] 2 tests from BoxDeformationTest (2572 ms total) 80: 80: [----------] 1 test from PositionRestraintCommTest 80: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any of the VCM groups 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any center of mass motion removal group. 80: This may lead to artifacts. 80: In most cases one should use one group for the whole system. 80: 80: Number of degrees of freedom in T-Coupling group System is 29527.73 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Channel_coco in octane membrane' 80: 10 steps, 0.0 ps. 80: Setting the LD random seed to -453580804 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 13 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.349 0.174 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 10.901 2.202 15.852 0.872 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (387 ms) 80: [----------] 1 test from PositionRestraintCommTest (387 ms total) 80: 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1124111447 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.95 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.010 193.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 44.795 0.536 1.929 0.012 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 2096660333 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.95 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 197.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 60.320 0.398 1.432 0.016 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 80: 80: 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (49379 ms) 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1341558437 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.95 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 194.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 59.601 0.403 1.450 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1740602366 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.95 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.013 0.007 196.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 65.872 0.364 1.312 0.018 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (65 ms) 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (49445 ms total) 80: 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 2147467006 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.012 0.006 197.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 71.649 0.335 1.206 0.005 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1009270787 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.012 0.006 197.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 69.671 0.344 1.240 0.005 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (29 ms) 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (29 ms total) 80: 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.010 0.005 197.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 151.107 0.159 0.572 0.038 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (19 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 198.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 86.276 0.278 1.001 0.022 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (22 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.087 0.043 199.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 17.916 1.340 4.823 0.005 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (64 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.069 0.035 199.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 22.516 1.066 3.837 0.006 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (50 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.083 0.042 199.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 18.635 1.288 4.637 0.005 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (57 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 80: Parrinello-Rahman is not implemented in md-vv. 80: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.010 0.005 197.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 149.281 0.161 0.579 0.038 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (19 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.010 0.005 197.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 160.396 0.150 0.539 0.041 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (17 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.009 0.004 197.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 178.380 0.135 0.484 0.045 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (17 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 197.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 186.841 0.128 0.462 0.048 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (28 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.009 0.004 197.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 174.654 0.137 0.495 0.044 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (29 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 197.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 186.605 0.129 0.463 0.048 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (29 ms) 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest (357 ms total) 80: 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -1212246148 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 197.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 401.143 0.060 0.431 0.014 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (9 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -436736129 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 197.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 376.159 0.064 0.459 0.013 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (9 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 712768219 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 197.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 396.799 0.060 0.435 0.014 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (9 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -67243010 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.009 0.005 197.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 334.392 0.072 0.517 0.012 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (9 ms) 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (39 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 31 tests from 9 test suites ran. (53628 ms total) 80: [ PASSED ] 30 tests. 80: [ SKIPPED ] 1 test, listed below: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80/104 Test #80: MdrunTestsOneRank ......................... Passed 53.64 sec test 81 Start 81: MdrunTestsTwoRanks 81: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 31 tests from 9 test suites. 81: [----------] Global test environment set-up. 81: [----------] 2 tests from AwhTest 81: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 6.2%. 81: The balanceable part of the MD step is 64%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 4.0%. 81: 81: 81: NOTE: 17 % of the run time was spent in domain decomposition, 81: 3 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 5 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.571 0.143 399.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 12.694 1.891 6.807 0.003 81: [ OK ] AwhTest.SingleBiasMultiDimCanRun (207 ms) 81: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 8.2%. 81: The balanceable part of the MD step is 75%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 6.1%. 81: 81: NOTE: 6.1 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 11 % of the run time was spent in domain decomposition, 81: 6 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.613 0.153 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 11.840 2.027 7.297 0.003 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 10.0%. 81: The balanceable part of the MD step is 79%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 7.9%. 81: 81: NOTE: 7.9 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.573 0.143 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 12.668 1.894 6.820 0.003 81: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (369 ms) 81: [----------] 2 tests from AwhTest (576 ms total) 81: 81: [----------] 1 test from CompelTest 81: [ RUN ] CompelTest.SwapCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Split0 group 'Ch0' contains 83 atoms. 81: Split1 group 'Ch1' contains 83 atoms. 81: Solvent group 'SOL' contains 11931 atoms. 81: Swap group 'NA+' contains 19 atoms. 81: Swap group 'CL-' contains 19 atoms. 81: Number of degrees of freedom in T-Coupling group System is 27869.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Determining initial numbers of ions per compartment. 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 2 steps, 0.0 ps. 81: Setting the LD random seed to -41964850 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning all bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.2%. 81: The balanceable part of the MD step is 22%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.5%. 81: 81: 81: NOTE: 23 % of the run time was spent in domain decomposition, 81: 22 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.722 0.181 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.743 4.179 60.178 0.230 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 81: 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Copying channel fluxes from checkpoint file data 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: NOTE: 19 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.424 0.106 399.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 9.776 2.455 35.353 0.391 81: [ OK ] CompelTest.SwapCanRun (601 ms) 81: [----------] 1 test from CompelTest (602 ms total) 81: 81: [----------] 6 tests from BondedInteractionsTest 81: [ RUN ] BondedInteractionsTest.NormalBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 45 % of the run time was spent in domain decomposition, 81: 14 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.080 0.020 399.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.287 5.598 20.154 0.000 81: Setting the LD random seed to -4440593 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalBondWorks (39 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 47 % of the run time was spent in domain decomposition, 81: 36 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.066 0.016 399.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.254 4.568 16.444 0.000 81: Setting the LD random seed to -1077259394 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedBondWorks (33 ms) 81: [ RUN ] BondedInteractionsTest.NormalAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 48 % of the run time was spent in domain decomposition, 81: 17 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.062 0.016 399.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.554 4.321 15.556 0.000 81: Setting the LD random seed to 2071822076 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalAngleWorks (32 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 44 % of the run time was spent in domain decomposition, 81: 32 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.064 0.016 399.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.358 4.479 16.125 0.000 81: Setting the LD random seed to -75891162 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (34 ms) 81: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 44 % of the run time was spent in domain decomposition, 81: 34 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.062 0.016 399.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.573 4.307 15.504 0.000 81: Setting the LD random seed to 1802466591 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalDihedralWorks (36 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 45 % of the run time was spent in domain decomposition, 81: 33 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.061 0.015 399.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.627 4.265 15.355 0.000 81: Setting the LD random seed to 2146826652 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (31 ms) 81: [----------] 6 tests from BondedInteractionsTest (208 ms total) 81: 81: [----------] 2 tests from BoxDeformationTest 81: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 39 % of the run time was spent in domain decomposition, 81: 17 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.063 0.016 395.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 10.860 2.210 15.912 0.001 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -85461269 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Setting gen_seed to -1635926146 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (36 ms) 81: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group rest is 1293.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 20 steps, 0.0 ps. 81: Setting the LD random seed to -144711297 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 81: 81: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 81: 81: Estimate for the relative computational load of the PME mesh part: 0.23 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB got disabled because it was unsuitable to use. 81: Average load imbalance: 19.3%. 81: The balanceable part of the MD step is 24%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 4.5%. 81: 81: 81: NOTE: 12 % of the run time was spent in domain decomposition, 81: 6 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.116 0.279 399.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 13.006 1.845 13.286 0.049 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2770 ms) 81: [----------] 2 tests from BoxDeformationTest (2806 ms total) 81: 81: [----------] 1 test from PositionRestraintCommTest 81: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any of the VCM groups 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any center of mass motion removal group. 81: This may lead to artifacts. 81: In most cases one should use one group for the whole system. 81: 81: Number of degrees of freedom in T-Coupling group System is 29527.73 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Channel_coco in octane membrane' 81: 10 steps, 0.0 ps. 81: Setting the LD random seed to -704653321 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 12 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.820 0.205 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 9.271 2.589 18.638 0.742 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (450 ms) 81: [----------] 1 test from PositionRestraintCommTest (450 ms total) 81: 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -203170178 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.95 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.390 0.097 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.432 5.415 19.495 0.001 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to 1039932903 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.95 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.083 0.021 397.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 20.683 1.160 4.177 0.006 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 81: 81: 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (49307 ms) 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -910258185 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.95 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.310 0.078 399.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.563 4.314 15.532 0.001 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -37069857 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.95 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 41 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.160 0.290 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 1.489 16.114 58.009 0.000 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (459 ms) 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (49767 ms total) 81: 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -43026442 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 19 % of the run time was spent in domain decomposition, 81: 9 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 17 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.331 0.083 399.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.219 4.599 16.556 0.000 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -184815951 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 15 % of the run time was spent in domain decomposition, 81: 10 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 14 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.245 0.061 399.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 7.042 3.408 12.269 0.000 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (244 ms) 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (244 ms total) 81: 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 9.1%. 81: The balanceable part of the MD step is 41%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 3.8%. 81: 81: 81: NOTE: 15 % of the run time was spent in domain decomposition, 81: 0 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 23 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.089 0.023 391.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 34.049 0.705 2.538 0.009 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (55 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 31.6%. 81: The balanceable part of the MD step is 46%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 14.5%. 81: 81: NOTE: 14.5 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 22 % of the run time was spent in domain decomposition, 81: 12 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.327 0.082 398.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 9.471 2.534 9.123 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (113 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 28.0%. 81: The balanceable part of the MD step is 46%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 12.8%. 81: 81: NOTE: 12.8 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 18 % of the run time was spent in domain decomposition, 81: 8 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.370 0.093 399.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 8.390 2.861 10.298 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (126 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 8.6%. 81: The balanceable part of the MD step is 55%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 4.7%. 81: 81: 81: NOTE: 17 % of the run time was spent in domain decomposition, 81: 5 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.391 0.098 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 7.948 3.020 10.871 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (126 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 22.3%. 81: The balanceable part of the MD step is 51%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 11.4%. 81: 81: NOTE: 11.4 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 17 % of the run time was spent in domain decomposition, 81: 7 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 10 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.377 0.095 399.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 8.224 2.918 10.506 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (120 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 81: Parrinello-Rahman is not implemented in md-vv. 81: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.338 0.085 398.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 9.161 2.620 9.431 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (111 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 10 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.350 0.088 397.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 8.833 2.717 9.782 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (115 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.372 0.093 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 8.354 2.873 10.343 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (116 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 38 % of the run time was spent in domain decomposition, 81: 7 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 23 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.096 0.024 395.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 32.100 0.748 2.692 0.008 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (65 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.038 0.010 397.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 80.941 0.297 1.067 0.021 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (45 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 13 % of the run time was spent in domain decomposition, 81: 6 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.292 0.073 399.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 10.622 2.259 8.134 0.003 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (117 ms) 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1114 ms total) 81: 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -1090625553 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 27.4%. 81: The balanceable part of the MD step is 42%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 11.4%. 81: 81: NOTE: 11.4 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 20 % of the run time was spent in domain decomposition, 81: 7 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 10 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.295 0.074 399.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 21.034 1.141 8.215 0.001 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (94 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -75181185 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 7.3%. 81: The balanceable part of the MD step is 49%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 3.5%. 81: 81: 81: NOTE: 11 % of the run time was spent in domain decomposition, 81: 5 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 29 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.686 0.172 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 9.061 2.649 19.071 0.000 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (196 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -906648009 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.1%. 81: The balanceable part of the MD step is 55%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.6%. 81: 81: 81: NOTE: 16 % of the run time was spent in domain decomposition, 81: 8 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.396 0.099 399.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 15.691 1.530 11.013 0.001 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (121 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -411042182 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 4.3%. 81: The balanceable part of the MD step is 56%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.4%. 81: 81: 81: NOTE: 17 % of the run time was spent in domain decomposition, 81: 9 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.347 0.087 399.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 17.917 1.340 9.645 0.001 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (107 ms) 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (520 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 31 tests from 9 test suites ran. (56375 ms total) 81: [ PASSED ] 30 tests. 81: [ SKIPPED ] 1 test, listed below: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81/104 Test #81: MdrunTestsTwoRanks ........................ Passed 56.40 sec test 82 Start 82: MdrunSingleRankAlgorithmsTests 82: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 82: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 600 82: [==========] Running 5 tests from 3 test suites. 82: [----------] Global test environment set-up. 82: [----------] 1 test from DispersionCorrectionTest 82: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 30.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: There are 9 non-linear virtual site constructions. Their contribution to 82: the energy error is approximated. In most cases this does not affect the 82: error significantly. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 82: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 82: 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Alanine dipeptide in vacuo' 82: 200 steps, 0.4 ps. 82: Setting the LD random seed to 2147405663 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Converted 3 Bonds with virtual sites to connections, 7 left 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 12 Constraints with virtual sites to connections, 0 left 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 199.1 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 1467.157 0.016 0.118 0.246 82: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (51 ms) 82: [----------] 1 test from DispersionCorrectionTest (51 ms total) 82: 82: [----------] 1 test from OriresTest 82: [ RUN ] OriresTest.OriresCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 518.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There was 1 NOTE 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2026.3-Debian_1 (single precision) 82: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 82: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 82: 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 82: 10 steps, 0.0 ps. 82: Setting the LD random seed to -34873889 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 82: 82: turning H bonds into constraints... 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/orires_1lvz.gro' 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.097 0.049 199.8 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 39.122 0.613 4.417 0.049 82: [ OK ] OriresTest.OriresCanRun (342 ms) 82: [----------] 1 test from OriresTest (342 ms total) 82: 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 82: Number of degrees of freedom in T-Coupling group rest is 10.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to 1644128981 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: Searching the wall atom type(s) 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.553 0.277 199.9 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 16.403 1.463 13.169 0.000 82: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 82: 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (119473 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 82: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 82: The supported numbers are > 1. 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 all molecules should be neutral. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 you can only use domain decomposition when there 82: are only small molecules with all bonds constrained (mdrun will check for 82: this). 82: 82: Number of degrees of freedom in T-Coupling group rest is 9.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to 1065349087 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 199.2 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 289.122 0.083 0.747 0.005 82: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (62334 ms) 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (181808 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 5 tests from 3 test suites ran. (182231 ms total) 82: [ PASSED ] 5 tests. 82/104 Test #82: MdrunSingleRankAlgorithmsTests ............ Passed 182.25 sec test 83 Start 83: Minimize1RankTests 83: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/Minimize1RankTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 2 test suites. 83: [----------] Global test environment set-up. 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -4.7990997e+01 83: Maximum force = 1.8629692e+02 on atom 13 83: Norm of force = 8.7721836e+01 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (258 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 3.02331e+02 on atom 3 83: F-Norm = 1.18024e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -5.5862350e+01 83: Maximum force = 4.2726685e+02 on atom 13 83: Norm of force = 1.8452681e+02 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (262 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.1937723e+02 83: Maximum force = 9.9988691e+03 on atom 9 83: Norm of force = 4.6167015e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (60 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: 83: NOTE 2 [file glycine_vacuo.top, line 12]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41575e+04 on atom 10 83: F-Norm = 1.18451e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.5174414e+02 83: Maximum force = 7.4208760e+03 on atom 9 83: Norm of force = 3.5692977e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (54 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.5698444e+02 83: Maximum force = 4.5702216e+02 on atom 17 83: Norm of force = 1.8327095e+02 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (26 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: 83: NOTE 3 [file unknown]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 1.06799e+03 on atom 28 83: F-Norm = 4.26914e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.6941290e+02 83: Maximum force = 2.1840109e+02 on atom 17 83: Norm of force = 7.9232004e+01 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (12 ms) 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (675 ms total) 83: 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents converged to Fmax < 10 in 1 steps 83: Potential Energy = -9.7425687e-01 83: Maximum force = 4.0132279e+00 on atom 1 83: Norm of force = 1.6383933e+00 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (8 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 83: Potential Energy = -9.9064195e-01 83: Maximum force = 2.5781672e+00 on atom 1 83: Norm of force = 1.0525324e+00 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (7 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 83: Potential Energy = -9.9064195e-01 83: Maximum force = 2.5781672e+00 on atom 1 83: Norm of force = 1.0525324e+00 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (6 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.1939691e+02 83: Maximum force = 9.9704258e+03 on atom 9 83: Norm of force = 4.6227543e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (53 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (single precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.5625757e+02 83: Maximum force = 7.5018242e+03 on atom 9 83: Norm of force = 3.6139019e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (52 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.3-Debian_1 (single precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization has stopped, but the forces have not converged to the 83: requested precision Fmax < 10 (which may not be possible for your system). It 83: stopped because the algorithm tried to make a new step whose size was too 83: small, or there was no change in the energy since last step. Either way, we 83: regard the minimization as converged to within the available machine 83: precision, given your starting configuration and EM parameters. 83: 83: Double precision normally gives you higher accuracy, but this is often not 83: needed for preparing to run molecular dynamics. 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 83: but did not reach the requested Fmax < 10. 83: Potential Energy = 5.6111578e+02 83: Maximum force = 1.2685379e+04 on atom 10 83: Norm of force = 6.0643592e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (52 ms) 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (180 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 2 test suites ran. (882 ms total) 83: [ PASSED ] 12 tests. 83/104 Test #83: Minimize1RankTests ........................ Passed 0.92 sec test 84 Start 84: Minimize2RankTests 84: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/Minimize2RankTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 12 tests from 2 test suites. 84: [----------] Global test environment set-up. 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -4.7990952e+01 84: Maximum force = 1.8629709e+02 on atom 13 84: Norm of force = 8.7721970e+01 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (344 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 3.02331e+02 on atom 3 84: F-Norm = 1.18024e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -5.5862202e+01 84: Maximum force = 4.2727243e+02 on atom 13 84: Norm of force = 1.8452909e+02 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (257 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.1937720e+02 84: Maximum force = 9.9988691e+03 on atom 9 84: Norm of force = 4.6167015e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (87 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: 84: NOTE 2 [file glycine_vacuo.top, line 12]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41575e+04 on atom 10 84: F-Norm = 1.18451e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.5174358e+02 84: Maximum force = 7.4208833e+03 on atom 9 84: Norm of force = 3.5692986e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (54 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.5698444e+02 84: Maximum force = 4.5702222e+02 on atom 17 84: Norm of force = 1.8327095e+02 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (57 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: 84: NOTE 3 [file unknown]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 1.06799e+03 on atom 28 84: F-Norm = 4.26914e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.6941260e+02 84: Maximum force = 2.1838724e+02 on atom 17 84: Norm of force = 7.9232344e+01 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (38 ms) 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (840 ms total) 84: 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents converged to Fmax < 10 in 1 steps 84: Potential Energy = -9.7425687e-01 84: Maximum force = 4.0132279e+00 on atom 3 84: Norm of force = 1.6383933e+00 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (11 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 4.01323e+00 on atom 3 84: F-Norm = 1.63839e+00 84: 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 84: Potential Energy = -9.9064195e-01 84: Maximum force = 2.5781672e+00 on atom 3 84: Norm of force = 1.0525324e+00 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (32 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.1939664e+02 84: Maximum force = 9.9704229e+03 on atom 9 84: Norm of force = 4.6227537e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (155 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (single precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41672e+04 on atom 10 84: F-Norm = 1.19357e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.5625771e+02 84: Maximum force = 7.5018237e+03 on atom 9 84: Norm of force = 3.6139019e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (157 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (49 ms) 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (410 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 12 tests from 2 test suites ran. (1271 ms total) 84: [ PASSED ] 12 tests. 84/104 Test #84: Minimize2RankTests ........................ Passed 1.29 sec test 85 Start 85: MdrunNonIntegratorTests 85: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 46 tests from 3 test suites. 85: [----------] Global test environment set-up. 85: [----------] 1 test from NonbondedBenchTest 85: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 85: SIMD width: 4 85: System size: 3000 atoms 85: Cut-off radius: 1 nm 85: Number of threads: 1 85: Number of iterations: 1 85: Compute energies: no 85: Ewald excl. corr.: analytical 85: 85: Coulomb LJ comb. SIMD intmod. Mcycles Mcycles/it. pairs/cycle 85: total useful 85: Ewald all geom. 4xM PotShift 0.266 0.2657 4.4805 2.3704 85: [ OK ] NonbondedBenchTest.BasicEndToEndTest (37 ms) 85: [----------] 1 test from NonbondedBenchTest (37 ms total) 85: 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.015 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 99.050 0.242 0.872 0.014 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 85: 85: trr version: GMX_trn_file (single precision) 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1933.645 0.012 0.045 0.269 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (30 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 181.520 0.132 0.476 0.025 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1428.709 0.017 0.060 0.198 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (26 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.006 197.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 228.458 0.105 0.378 0.032 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 35 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 192.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1018.280 0.024 0.085 0.141 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (25 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 138.415 0.173 0.624 0.019 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1713.656 0.014 0.050 0.238 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (28 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 188.981 0.127 0.457 0.033 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 189.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3702.280 0.006 0.023 0.643 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (300 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 203.226 0.118 0.425 0.035 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 25 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 189.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4085.274 0.006 0.021 0.709 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (256 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 197.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 278.924 0.086 0.310 0.048 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 28 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 189.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3496.364 0.007 0.025 0.607 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (262 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.290 0.145 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 10.128 2.370 8.531 0.002 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1284.795 0.019 0.067 0.223 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (431 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.338 0.169 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 8.697 2.759 9.934 0.003 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 44 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.005 0.002 195.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 600.975 0.040 0.144 0.202 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (261 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 198.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 108.081 0.222 0.799 0.036 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1280.256 0.019 0.067 0.430 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (76 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 193.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 201.465 0.119 0.429 0.068 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 37 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1438.383 0.017 0.060 0.483 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (123 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.007 196.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 215.232 0.112 0.401 0.072 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 192.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 983.492 0.024 0.088 0.330 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (67 ms) 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1893 ms total) 85: 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.035 0.017 198.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 83.941 0.286 1.029 0.035 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.004 0.002 183.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 751.292 0.032 0.115 0.313 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (54 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 197.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 187.531 0.128 0.461 0.078 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 181.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 954.243 0.025 0.091 0.398 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (38 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 197.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 190.247 0.126 0.454 0.079 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1299.703 0.018 0.066 0.542 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (31 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 197.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 207.665 0.116 0.416 0.087 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1308.537 0.018 0.066 0.545 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (29 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 197.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 211.813 0.113 0.408 0.088 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 173.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1376.669 0.017 0.063 0.574 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (25 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 197.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 176.042 0.136 0.491 0.073 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 178.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1461.241 0.016 0.059 0.609 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (25 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 124.620 0.193 0.693 0.052 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 178.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1217.990 0.020 0.071 0.507 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (29 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 198.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 214.378 0.112 0.403 0.089 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1724.208 0.014 0.050 0.718 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.010 198.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 142.024 0.169 0.608 0.059 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1300.801 0.018 0.066 0.542 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (28 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.007 197.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 224.291 0.107 0.385 0.093 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1386.584 0.017 0.062 0.578 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.007 197.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 220.076 0.109 0.393 0.092 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 176.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1696.199 0.014 0.051 0.707 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 198.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 192.230 0.125 0.449 0.080 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 180.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1376.054 0.017 0.063 0.573 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (24 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 198.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 209.409 0.115 0.413 0.087 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 178.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1362.059 0.018 0.063 0.568 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 207.121 0.116 0.417 0.086 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 10 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 187.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 856.233 0.028 0.101 0.357 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (23 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 198.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 208.890 0.115 0.414 0.087 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 180.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1401.090 0.017 0.062 0.584 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.007 198.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 217.543 0.110 0.397 0.091 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 178.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1377.593 0.017 0.063 0.574 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (22 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.007 198.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 216.002 0.111 0.400 0.090 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1664.126 0.014 0.052 0.693 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (21 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 198.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 192.242 0.125 0.449 0.080 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 176.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1008.446 0.024 0.086 0.420 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (28 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 187.549 0.128 0.461 0.078 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1309.928 0.018 0.066 0.546 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (29 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.009 198.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 172.084 0.139 0.502 0.072 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 18 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 176.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1692.006 0.014 0.051 0.705 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (27 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 147.115 0.163 0.587 0.061 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 832.963 0.029 0.104 0.347 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (30 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 136.263 0.176 0.634 0.057 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1173.446 0.020 0.074 0.489 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 198.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 191.626 0.125 0.451 0.080 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 182.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1210.809 0.020 0.071 0.505 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (33 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.009 198.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 170.065 0.141 0.508 0.071 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 173.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1425.403 0.017 0.061 0.594 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (34 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.007 198.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 215.987 0.111 0.400 0.090 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 177.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1451.601 0.017 0.060 0.605 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (30 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.013 0.007 198.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 225.646 0.106 0.383 0.094 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 186.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 840.005 0.029 0.103 0.350 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (31 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 165.781 0.145 0.521 0.069 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 23 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 187.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 853.623 0.028 0.101 0.356 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 197.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 210.784 0.114 0.410 0.088 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 175.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1500.754 0.016 0.058 0.625 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (30 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.009 198.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 166.985 0.144 0.517 0.070 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 25 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1182.910 0.020 0.073 0.493 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 198.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 152.042 0.158 0.568 0.063 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 174.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1568.379 0.015 0.055 0.653 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (33 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.009 198.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 166.723 0.144 0.518 0.069 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 173.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1513.288 0.016 0.057 0.631 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (31 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 198.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 161.116 0.149 0.536 0.067 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1167.000 0.021 0.074 0.486 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (32 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 198.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 208.940 0.115 0.414 0.087 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 175.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1509.949 0.016 0.057 0.629 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (30 ms) 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (974 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 46 tests from 3 test suites ran. (2933 ms total) 85: [ PASSED ] 46 tests. 85/104 Test #85: MdrunNonIntegratorTests ................... Passed 2.96 sec test 86 Start 86: MdrunTpiTests 86: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunTpiTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 3 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 3 tests from Simple/TpiTest 86: [ RUN ] Simple/TpiTest.ReproducesOutput/0 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2026.3-Debian_1 (single precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/0 (299 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/1 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2026.3-Debian_1 (single precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/1 (244 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/2 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2026.3-Debian_1 (single precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/2 (252 ms) 86: [----------] 3 tests from Simple/TpiTest (796 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 3 tests from 1 test suite ran. (813 ms total) 86: [ PASSED ] 3 tests. 86/104 Test #86: MdrunTpiTests ............................. Passed 0.84 sec test 87 Start 87: MdrunMpiTests 87: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunMpiTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 16 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from MimicTest 87: [ RUN ] MimicTest.OneQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 64 % of the run time was spent in domain decomposition, 87: 11 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.084 0.021 399.1 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 4.111 5.838 21.018 0.001 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1996292063 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.OneQuantumMol (39 ms) 87: [ RUN ] MimicTest.AllQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 58 % of the run time was spent in domain decomposition, 87: 15 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.122 0.030 399.6 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 2.834 8.468 30.485 0.000 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -527625 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.AllQuantumMol (64 ms) 87: [ RUN ] MimicTest.TwoQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 92 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.046 0.012 398.8 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 7.476 3.210 11.556 0.001 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -72900867 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.TwoQuantumMol (46 ms) 87: [ RUN ] MimicTest.BondCuts 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 66.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: NVE simulation: will use the initial temperature of 300.368 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 87: 87: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 45 % of the run time was spent in domain decomposition, 87: 30 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.083 0.021 397.1 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 4.155 5.776 20.793 0.001 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -71827457 87: 87: Generated 2211 of the 2211 non-bonded parameter combinations 87: 87: Generated 2211 of the 2211 1-4 parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.BondCuts (52 ms) 87: [----------] 4 tests from MimicTest (204 ms total) 87: 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: There was 1 NOTE 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There were 2 NOTEs 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There was 1 NOTE 87: Setting the LD random seed to -663029769 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to 1786705618 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -625022753 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -269756465 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was turned on during the run due to measured imbalance. 87: Average load imbalance: 17.4%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 8.7%. 87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 87: 87: NOTE: 8.7 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: NOTE: 17 % of the run time was spent in domain decomposition, 87: 9 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.539 0.135 399.5 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 13.460 1.783 6.419 0.001 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (153 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 7 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.267 0.067 398.8 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 27.102 0.886 3.188 0.002 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (82 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 4.4%. 87: The balanceable part of the MD step is 29%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.3%. 87: 87: 87: NOTE: 12 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.209 0.303 399.2 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 5.991 4.006 14.422 0.000 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (20566 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.773 0.193 399.8 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 9.387 2.557 9.204 0.001 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (11860 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.796 0.199 399.4 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 9.105 2.636 9.489 0.001 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (245 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.3-Debian_1 (single precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.385 0.097 397.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 18.759 1.279 4.606 0.001 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (126 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (33037 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 16 tests from 2 test suites ran. (33273 ms total) 87: [ PASSED ] 10 tests. 87: [ SKIPPED ] 6 tests, listed below: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87/104 Test #87: MdrunMpiTests ............................. Passed 33.29 sec test 88 Start 88: MdrunMultiSimTests 88: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 2 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from InNvt/MultiSimTerminationTest 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 88: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 2 tests from 1 test suite ran. (8 ms total) 88: [ PASSED ] 2 tests. 88: 88: YOU HAVE 4 DISABLED TESTS 88: 88/104 Test #88: MdrunMultiSimTests ........................ Passed 0.03 sec test 89 Start 89: MdrunMultiSimReplexTests 89: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 1 test from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 89: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 89: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 1 test from 1 test suite ran. (9 ms total) 89: [ PASSED ] 1 test. 89: 89: YOU HAVE 4 DISABLED TESTS 89: 89/104 Test #89: MdrunMultiSimReplexTests .................. Passed 0.04 sec test 90 Start 90: MdrunMultiSimReplexEquivalenceTests 90: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 0 tests from 0 test suites. 90: [==========] 0 tests from 0 test suites ran. (0 ms total) 90: [ PASSED ] 0 tests. 90: 90: YOU HAVE 10 DISABLED TESTS 90: 90/104 Test #90: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.04 sec test 91 Start 91: MdrunMpi1RankPmeTests 91: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 91: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 19 tests from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 19 tests from ReproducesEnergies/PmeTest 91: Number of degrees of freedom in T-Coupling group rest is 12.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 1046.791 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 2 NOTEs 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: For a correct single-point energy evaluation with nsteps = 0, use 91: continuation = yes to avoid constraining the input coordinates. 91: 91: Number of degrees of freedom in T-Coupling group rest is 13.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 966.268 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 3 NOTEs 91: Setting the LD random seed to -1354892453 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: Setting the LD random seed to -674239297 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: Searching the wall atom type(s) 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.727 0.363 200.0 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 4.993 4.807 17.305 0.000 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (24832 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 10 % of the run time was spent in domain decomposition, 91: 2 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.595 0.297 199.9 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 6.100 3.935 14.165 0.000 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (331 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: NOTE: 32 % of the run time was spent in domain decomposition, 91: 5 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.081 0.041 199.7 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 2.133 11.252 40.508 0.000 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (93634 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 21 % of the run time was spent in domain decomposition, 91: 3 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.127 0.063 199.8 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 28.628 0.838 3.018 0.002 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (97 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [----------] 19 tests from ReproducesEnergies/PmeTest (118896 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 19 tests from 1 test suite ran. (118922 ms total) 91: [ PASSED ] 4 tests. 91: [ SKIPPED ] 15 tests, listed below: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91/104 Test #91: MdrunMpi1RankPmeTests ..................... Passed 118.96 sec test 92 Start 92: MdrunMpi2RankPmeTests 92: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 19 tests from 1 test suite. 92: [----------] Global test environment set-up. 92: [----------] 19 tests from ReproducesEnergies/PmeTest 92: Number of degrees of freedom in T-Coupling group rest is 12.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 1046.791 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 2 NOTEs 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: For a correct single-point energy evaluation with nsteps = 0, use 92: continuation = yes to avoid constraining the input coordinates. 92: 92: Number of degrees of freedom in T-Coupling group rest is 13.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 966.268 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 3 NOTEs 92: Setting the LD random seed to -26286485 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: Setting the LD random seed to 1584397815 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: Searching the wall atom type(s) 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 23.6%. 92: The balanceable part of the MD step is 21%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 4.9%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: 92: 92: NOTE: 20 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 2.349 0.587 400.0 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 3.090 7.768 27.965 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (28454 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 6.3%. 92: The balanceable part of the MD step is 1%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.0%. 92: 92: 92: NOTE: 22 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.437 0.109 399.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 16.574 1.448 5.213 0.001 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (157 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 14 % of the run time was spent in domain decomposition, 92: 18 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 20 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.207 0.052 399.4 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 1.668 14.387 51.793 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (101400 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.797 0.199 399.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 9.100 2.637 9.494 0.001 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (16056 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.726 0.182 399.8 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 9.996 2.401 8.643 0.001 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (238 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 29 % of the run time was spent in domain decomposition, 92: 5 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.077 0.019 398.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 4.473 5.365 19.314 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (65670 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 18.0%. 92: The balanceable part of the MD step is 24%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 4.4%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.361 0.340 399.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 5.331 4.502 16.206 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (418 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [----------] 19 tests from ReproducesEnergies/PmeTest (212399 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 19 tests from 1 test suite ran. (212448 ms total) 92: [ PASSED ] 7 tests. 92: [ SKIPPED ] 12 tests, listed below: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92/104 Test #92: MdrunMpi2RankPmeTests ..................... Passed 212.48 sec test 93 Start 93: MdrunMpi4RankPmeTests 93: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "1" "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunMpi4RankPmeTests.xml" 93: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 93: Test timeout computed to be: 600 93: [==========] Running 19 tests from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 19 tests from ReproducesEnergies/PmeTest 93: Number of degrees of freedom in T-Coupling group rest is 12.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 1046.791 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 2 NOTEs 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: For a correct single-point energy evaluation with nsteps = 0, use 93: continuation = yes to avoid constraining the input coordinates. 93: 93: Number of degrees of freedom in T-Coupling group rest is 13.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 966.268 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 3 NOTEs 93: Setting the LD random seed to -546832386 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: Setting the LD random seed to 1545321975 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: Searching the wall atom type(s) 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 19.7%. 93: The balanceable part of the MD step is 7%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 1.4%. 93: 93: 93: NOTE: 67 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.096 0.024 398.7 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 75.593 0.317 1.143 0.005 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (33465 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 31.7%. 93: The balanceable part of the MD step is 2%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.8%. 93: 93: 93: NOTE: 22 % of the run time was spent in domain decomposition, 93: 0 % of the run time was spent in pair search, 93: you might want to increase nstlist (this has no effect on accuracy) 93: 93: NOTE: 16 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.595 0.149 399.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 12.184 1.970 7.092 0.001 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (783 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: NOTE: 12 % of the run time was spent in domain decomposition, 93: 2 % of the run time was spent in pair search, 93: you might want to increase nstlist (this has no effect on accuracy) 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.003 0.001 346.3 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 104.540 0.230 0.826 0.007 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (100559 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was turned on during the run due to measured imbalance. 93: Average load imbalance: 13.2%. 93: The balanceable part of the MD step is 60%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 7.9%. 93: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 93: Average PME mesh/force load: 0.053 93: Part of the total run time spent waiting due to PP/PME imbalance: 6.7 % 93: 93: NOTE: 7.9 % of the available CPU time was lost due to load imbalance 93: in the domain decomposition. 93: You can consider manually changing the decomposition (option -dd); 93: e.g. by using fewer domains along the box dimension in which there is 93: considerable inhomogeneity in the simulated system. 93: NOTE: 6.7 % performance was lost because the PME ranks 93: had less work to do than the PP ranks. 93: You might want to decrease the number of PME ranks 93: or decrease the cut-off and the grid spacing. 93: 93: 93: NOTE: 14 % of the run time was spent in domain decomposition, 93: 0 % of the run time was spent in pair search, 93: you might want to increase nstlist (this has no effect on accuracy) 93: 93: NOTE: 36 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 2.656 0.680 390.6 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 2.668 8.994 32.379 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (14112 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 6.5%. 93: The balanceable part of the MD step is 43%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 2.8%. 93: Average PME mesh/force load: 1.356 93: Part of the total run time spent waiting due to PP/PME imbalance: 2.3 % 93: 93: 93: NOTE: 18 % of the run time was spent in domain decomposition, 93: 0 % of the run time was spent in pair search, 93: you might want to increase nstlist (this has no effect on accuracy) 93: 93: NOTE: 34 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.569 0.142 399.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 12.746 1.883 6.779 0.001 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (799 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.008 0.002 351.4 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 36.968 0.649 2.337 0.003 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (25250 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was turned on during the run due to measured imbalance. 93: Average load imbalance: 19.8%. 93: The balanceable part of the MD step is 15%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 2.9%. 93: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 93: 93: 93: NOTE: 24 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 1.162 0.306 379.2 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 5.923 4.052 14.588 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (1012 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [----------] 19 tests from ReproducesEnergies/PmeTest (175985 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 19 tests from 1 test suite ran. (176006 ms total) 93: [ PASSED ] 7 tests. 93: [ SKIPPED ] 12 tests, listed below: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93/104 Test #93: MdrunMpi4RankPmeTests ..................... Passed 176.02 sec test 94 Start 94: MdrunCoordinationBasicTests1Rank 94: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 94: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 94: Test timeout computed to be: 1920 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest 94: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.013 0.013 99.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 113.786 0.211 0.759 0.016 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.007 0.007 99.4 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 198.492 0.121 0.435 0.028 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 4. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 4. 94: 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.005 0.005 98.5 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 314.044 0.076 0.275 0.044 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.009 0.009 98.9 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 166.435 0.144 0.519 0.023 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.010 0.010 99.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 149.283 0.161 0.579 0.021 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.017 0.017 99.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 87.201 0.275 0.991 0.012 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (127 ms) 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest (127 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (143 ms total) 94: [ PASSED ] 1 test. 94/104 Test #94: MdrunCoordinationBasicTests1Rank .......... Passed 0.18 sec test 95 Start 95: MdrunCoordinationBasicTests2Ranks 95: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 95: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 95: Test timeout computed to be: 1920 95: [==========] Running 1 test from 1 test suite. 95: [----------] Global test environment set-up. 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest 95: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.7%. 95: The balanceable part of the MD step is 49%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.9%. 95: 95: 95: NOTE: 55 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.031 0.015 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 95.871 0.250 0.901 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.8%. 95: The balanceable part of the MD step is 47%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.8%. 95: 95: 95: NOTE: 60 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.031 0.016 199.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 94.122 0.255 0.918 0.013 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 2.3%. 95: The balanceable part of the MD step is 42%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 1.0%. 95: 95: 95: NOTE: 82 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.026 0.029 89.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 50.885 0.472 1.698 0.007 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 2.5%. 95: The balanceable part of the MD step is 36%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.9%. 95: 95: 95: NOTE: 63 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.041 0.025 164.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 59.099 0.406 1.462 0.008 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was turned on during the run due to measured imbalance. 95: Average load imbalance: 18.8%. 95: The balanceable part of the MD step is 49%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 9.3%. 95: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 95: 95: NOTE: 9.3 % of the available CPU time was lost due to load imbalance 95: in the domain decomposition. 95: You can consider manually changing the decomposition (option -dd); 95: e.g. by using fewer domains along the box dimension in which there is 95: considerable inhomogeneity in the simulated system. 95: 95: NOTE: 14 % of the run time was spent in domain decomposition, 95: 0 % of the run time was spent in pair search, 95: you might want to increase nstlist (this has no effect on accuracy) 95: 95: NOTE: 46 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.404 0.202 199.9 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 7.270 3.301 11.884 0.001 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 2.2%. 95: The balanceable part of the MD step is 41%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.9%. 95: 95: 95: NOTE: 85 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.043 0.037 116.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 40.146 0.598 2.152 0.006 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1396 ms) 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1396 ms total) 95: 95: [----------] Global test environment tear-down 95: [==========] 1 test from 1 test suite ran. (1417 ms total) 95: [ PASSED ] 1 test. 95/104 Test #95: MdrunCoordinationBasicTests2Ranks ......... Passed 1.45 sec test 96 Start 96: MdrunCoordinationCouplingTests1Rank 96: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 96: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 96: Test timeout computed to be: 1920 96: [==========] Running 25 tests from 1 test suite. 96: [----------] Global test environment set-up. 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 116.211 0.207 0.743 0.016 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 243.367 0.099 0.355 0.034 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 97.597 0.246 0.885 0.014 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 129.188 0.186 0.669 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 138.148 0.174 0.625 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 114.208 0.210 0.757 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (144 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 229.069 0.105 0.377 0.032 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.022 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 67.420 0.356 1.282 0.009 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 98.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 216.953 0.111 0.398 0.030 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 145.585 0.165 0.593 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.024 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 61.945 0.387 1.395 0.009 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 174.833 0.137 0.494 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (159 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 205.882 0.117 0.420 0.029 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 134.276 0.179 0.643 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.364 0.112 0.403 0.030 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 136.408 0.176 0.633 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 178.139 0.135 0.485 0.025 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 152.902 0.157 0.565 0.021 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (112 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 184.847 0.130 0.467 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 165.973 0.145 0.521 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 146.020 0.164 0.592 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 98.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 230.794 0.104 0.374 0.032 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 158.013 0.152 0.547 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 176.775 0.136 0.489 0.025 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (136 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 98.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 321.836 0.075 0.268 0.045 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 323.085 0.074 0.267 0.045 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 184.925 0.130 0.467 0.026 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 167.704 0.143 0.515 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 164.383 0.146 0.526 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 208.163 0.115 0.415 0.029 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (106 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 235.371 0.102 0.367 0.033 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 171.700 0.140 0.503 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 196.629 0.122 0.439 0.027 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.019 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 78.084 0.307 1.107 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 252.504 0.095 0.342 0.035 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 128.423 0.187 0.673 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (121 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.145 0.126 0.452 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 205.868 0.117 0.420 0.029 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 203.609 0.118 0.424 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.506 0.123 0.442 0.027 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 141.101 0.170 0.612 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 147.425 0.163 0.586 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (98 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 98.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 294.751 0.081 0.293 0.041 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.679 0.129 0.463 0.026 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 145.955 0.164 0.592 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.878 0.243 0.874 0.014 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 125.279 0.192 0.690 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.017 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.545 0.271 0.976 0.012 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (132 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 97.367 0.246 0.887 0.014 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 291.888 0.082 0.296 0.041 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.021 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 68.936 0.348 1.253 0.010 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 113.568 0.211 0.761 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 116.848 0.205 0.739 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 104.879 0.229 0.824 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (134 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.025 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 59.566 0.403 1.450 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 260.876 0.092 0.331 0.036 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 318.032 0.075 0.272 0.044 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.912 0.250 0.901 0.013 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 108.887 0.220 0.793 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.022 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 65.879 0.364 1.311 0.009 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (148 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 196.585 0.122 0.440 0.027 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.549 0.117 0.422 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 162.596 0.148 0.531 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 159.630 0.150 0.541 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 249.973 0.096 0.346 0.035 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.037 0.037 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 40.108 0.598 2.154 0.006 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (152 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 257.927 0.093 0.335 0.036 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 208.728 0.115 0.414 0.029 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 220.297 0.109 0.392 0.031 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 169.779 0.141 0.509 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 99.604 0.241 0.867 0.014 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.016 0.016 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 89.517 0.268 0.965 0.012 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (146 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 106.148 0.226 0.814 0.015 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.230 0.244 0.880 0.014 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 96.476 0.249 0.896 0.013 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 127.253 0.189 0.679 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 137.000 0.175 0.631 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 166.273 0.144 0.520 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (115 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 99.620 0.241 0.867 0.014 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.896 0.117 0.422 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 147.168 0.163 0.587 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 284.830 0.084 0.303 0.040 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 146.249 0.164 0.591 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.018 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 81.084 0.296 1.066 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (116 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.017 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 86.498 0.277 0.999 0.012 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.010 53.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 141.055 0.170 0.613 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 98.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 399.183 0.060 0.216 0.055 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 244.993 0.098 0.353 0.034 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 138.565 0.173 0.624 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 156.376 0.153 0.553 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (124 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 303.897 0.079 0.284 0.042 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 170.569 0.141 0.507 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 205.985 0.117 0.419 0.029 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 307.369 0.078 0.281 0.043 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.020 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 73.411 0.327 1.177 0.010 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 154.316 0.156 0.560 0.021 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (114 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 156.178 0.154 0.553 0.022 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 155.370 0.154 0.556 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 123.355 0.195 0.700 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 187.995 0.128 0.460 0.026 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 161.543 0.149 0.535 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.028 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 52.256 0.459 1.653 0.007 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (124 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 129.639 0.185 0.666 0.018 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.028 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 52.524 0.457 1.645 0.007 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 312.435 0.077 0.277 0.043 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 276.272 0.087 0.313 0.038 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.019 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 78.292 0.307 1.104 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 102.327 0.235 0.844 0.014 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (135 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 108.860 0.220 0.794 0.015 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.602 0.251 0.904 0.013 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 135.714 0.177 0.637 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.021 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 69.884 0.343 1.236 0.010 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.027 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 54.393 0.441 1.588 0.008 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.019 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 78.374 0.306 1.102 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (140 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 108.400 0.221 0.797 0.015 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 98.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 359.197 0.067 0.241 0.050 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 98.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 314.814 0.076 0.274 0.044 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.025 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 57.623 0.417 1.499 0.008 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 123.407 0.194 0.700 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 40 % of the run time was spent in pair search, 96: you might want to increase nstlist (this has no effect on accuracy) 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 142.103 0.169 0.608 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (126 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 282.661 0.085 0.306 0.039 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 175.561 0.137 0.492 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 130.673 0.184 0.661 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 132.290 0.181 0.653 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 150.313 0.160 0.575 0.021 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.016 0.016 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 89.467 0.268 0.966 0.012 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (113 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 160.203 0.150 0.539 0.022 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 98.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 307.737 0.078 0.281 0.043 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 113.551 0.211 0.761 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 144.540 0.166 0.598 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 140.103 0.171 0.617 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 144.057 0.167 0.600 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (109 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 182.877 0.131 0.472 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.009 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 172.036 0.140 0.502 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 136.780 0.175 0.632 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 240.714 0.100 0.359 0.033 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.006 99.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 265.200 0.090 0.326 0.037 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 168.083 0.143 0.514 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (109 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.023 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 63.704 0.377 1.356 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.019 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 79.196 0.303 1.091 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 180.615 0.133 0.478 0.025 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 114.307 0.210 0.756 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 113.700 0.211 0.760 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.465 0.125 0.451 0.027 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (141 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.010 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 154.046 0.156 0.561 0.021 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 98.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 253.606 0.095 0.341 0.035 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 98.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 371.814 0.065 0.232 0.052 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 214.438 0.112 0.403 0.030 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 134.227 0.179 0.644 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 137.562 0.174 0.628 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (118 ms) 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (3187 ms total) 96: 96: [----------] Global test environment tear-down 96: [==========] 25 tests from 1 test suite ran. (3204 ms total) 96: [ PASSED ] 25 tests. 96/104 Test #96: MdrunCoordinationCouplingTests1Rank ....... Passed 3.24 sec test 97 Start 97: MdrunCoordinationCouplingTests2Ranks 97: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 97: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 97: Test timeout computed to be: 1920 97: [==========] Running 25 tests from 1 test suite. 97: [----------] Global test environment set-up. 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 42.3%. 97: The balanceable part of the MD step is 9%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 4.0%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: NOTE: 35 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.067 0.034 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 43.506 0.552 1.986 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.009 0.005 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 312.713 0.077 0.276 0.043 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.6%. 97: The balanceable part of the MD step is 32%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 172.985 0.139 0.499 0.024 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 49.9%. 97: The balanceable part of the MD step is 28%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 13.9%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 13.9 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 26 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 17 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.880 0.456 193.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.221 7.450 26.821 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 41.0%. 97: The balanceable part of the MD step is 15%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 6.2%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 6.2 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 42 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.031 0.015 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 95.646 0.251 0.903 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.7%. 97: The balanceable part of the MD step is 34%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 148.102 0.162 0.583 0.021 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1238 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 65 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.021 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 68.822 0.349 1.255 0.010 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.7%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 84 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.027 0.030 92.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 49.697 0.483 1.739 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.7%. 97: The balanceable part of the MD step is 3%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.0%. 97: 97: 97: NOTE: 31 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 55 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.040 0.033 122.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 44.964 0.534 1.922 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.8%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: NOTE: 84 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.037 113.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 39.633 0.606 2.180 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 38%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.038 0.019 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 77.419 0.310 1.116 0.011 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.6%. 97: The balanceable part of the MD step is 38%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 78 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.041 0.021 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 71.241 0.337 1.213 0.010 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (908 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 50%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 61 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 97.880 0.245 0.883 0.014 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.8%. 97: The balanceable part of the MD step is 32%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 60 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.109 0.071 154.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 20.791 1.154 4.156 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 37%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 158.423 0.151 0.545 0.022 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 34%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.5%. 97: 97: 97: NOTE: 74 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.049 0.041 121.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 36.116 0.665 2.392 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.8%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 238.132 0.101 0.363 0.033 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.7%. 97: The balanceable part of the MD step is 38%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 164.307 0.146 0.526 0.023 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (991 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 49%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 245.623 0.098 0.352 0.034 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.047 0.024 199.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 62.071 0.387 1.392 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 40%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.008 0.004 196.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 380.507 0.063 0.227 0.053 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.9%. 97: The balanceable part of the MD step is 40%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.024 0.012 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 122.688 0.196 0.704 0.017 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 18.7%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 9.5%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 9.5 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 15 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 43 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.240 0.626 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.347 10.227 36.819 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 3.1%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: NOTE: 66 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.023 199.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 64.450 0.372 1.341 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1876 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 62 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 195.957 0.122 0.441 0.027 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 26 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 35 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.026 0.013 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 113.443 0.212 0.762 0.016 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 53 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 197.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 194.411 0.123 0.444 0.027 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 132.362 0.181 0.653 0.018 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.824 0.428 192.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.432 6.993 25.174 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 17 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.114 0.057 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 25.631 0.936 3.371 0.004 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2750 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 17 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 35 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.415 0.208 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 7.073 3.393 12.215 0.001 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 43 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.008 0.004 196.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 345.373 0.069 0.250 0.048 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 62 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.012 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 126.450 0.190 0.683 0.018 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.981 0.493 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.980 8.054 28.993 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.033 0.017 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 88.448 0.271 0.977 0.012 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.010 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 141.400 0.170 0.611 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2483 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.052 0.026 199.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 56.845 0.422 1.520 0.008 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.956 0.152 0.547 0.022 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.009 192.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 167.987 0.143 0.514 0.023 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.010 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 141.722 0.169 0.610 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.027 0.014 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 108.584 0.221 0.796 0.015 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.828 0.130 0.467 0.026 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (784 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 21 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 33 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.404 0.206 196.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 7.133 3.365 12.113 0.001 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.115 0.058 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 25.421 0.944 3.399 0.004 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 29 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.164 0.082 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 17.922 1.339 4.821 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 196.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 232.151 0.103 0.372 0.032 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.792 0.398 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.692 6.500 23.401 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.973 0.486 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.019 7.949 28.615 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (4224 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 257.335 0.093 0.336 0.036 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 88 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.038 0.023 165.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 64.202 0.374 1.346 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 79 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.052 0.044 118.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.422 0.718 2.585 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 79 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 7 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.070 0.035 199.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 41.904 0.573 2.062 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 51 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 215.353 0.111 0.401 0.030 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 16 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 38 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.335 0.168 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 8.768 2.737 9.854 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1681 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.034 0.017 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 87.095 0.276 0.992 0.012 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 38 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 193.468 0.124 0.447 0.027 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 177.467 0.135 0.487 0.025 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 64 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.046 0.023 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 62.964 0.381 1.372 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 65 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.053 0.027 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 55.241 0.434 1.564 0.008 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 27 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 34 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 193.504 0.124 0.447 0.027 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (465 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 52 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 185.594 0.129 0.466 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 59 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 143.870 0.167 0.601 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 64 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.012 189.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 125.115 0.192 0.691 0.017 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 192.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 192.645 0.125 0.448 0.027 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 66 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.036 0.026 141.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 56.818 0.422 1.521 0.008 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 67 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 142.911 0.168 0.605 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (306 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 133.366 0.180 0.648 0.019 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 197.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 190.092 0.126 0.455 0.026 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 180.623 0.133 0.478 0.025 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.010 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 140.053 0.171 0.617 0.019 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 99.336 0.242 0.870 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 62 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 216.059 0.111 0.400 0.030 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (565 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 97.220 0.247 0.889 0.014 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 79 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.027 0.029 91.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 50.076 0.479 1.725 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 183.854 0.131 0.470 0.026 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 150.313 0.160 0.575 0.021 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 23 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.596 0.298 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 4.926 4.872 17.539 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 43 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.093 0.047 199.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 31.511 0.762 2.742 0.004 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2280 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.809 0.128 0.460 0.026 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 57 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.010 0.005 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 292.707 0.082 0.295 0.041 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 86 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.027 0.029 91.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 50.033 0.480 1.727 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 60 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 213.435 0.112 0.405 0.030 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 55 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.260 0.639 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.300 10.435 37.564 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 13 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.438 0.219 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 6.711 3.576 12.875 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (2806 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 40 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.015 144.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 99.419 0.241 0.869 0.014 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 63 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 207.543 0.116 0.416 0.029 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 57 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 223.093 0.108 0.387 0.031 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 58 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 20 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.024 0.012 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 123.779 0.194 0.698 0.017 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 52 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.118 0.059 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 24.900 0.964 3.470 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 260.408 0.092 0.332 0.036 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (844 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 76 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.035 0.034 104.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 43.802 0.548 1.973 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 186.665 0.129 0.463 0.026 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.008 0.004 197.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 342.369 0.070 0.252 0.048 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 60 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 215.915 0.111 0.400 0.030 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.410 0.205 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 7.163 3.350 12.062 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 101.289 0.237 0.853 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1477 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.8%. 97: The balanceable part of the MD step is 55%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.5%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 194.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 150.246 0.160 0.575 0.021 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 54%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 9 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.022 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 66.423 0.361 1.301 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 27.2%. 97: The balanceable part of the MD step is 52%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 14.1%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 14.1 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 13 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 34 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.428 0.714 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.057 11.670 42.013 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 5.0%. 97: The balanceable part of the MD step is 13%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.445 0.223 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 6.596 3.639 13.099 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 39.9%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 15.8%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 15.8 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 13 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 22 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.440 0.736 195.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.996 12.022 43.278 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 42%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.032 0.016 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 91.854 0.261 0.941 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (3630 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.8%. 97: The balanceable part of the MD step is 53%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.054 0.028 196.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 53.388 0.450 1.618 0.007 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 54%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.022 107.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 67.997 0.353 1.271 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.032 0.016 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 92.558 0.259 0.933 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 10.6%. 97: The balanceable part of the MD step is 65%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 6.9%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 6.9 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 2.193 1.102 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.333 18.004 64.816 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 44%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 196.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 98.170 0.244 0.880 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.4%. 97: The balanceable part of the MD step is 44%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.055 0.027 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 53.598 0.448 1.612 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (3525 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.4%. 97: The balanceable part of the MD step is 54%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.3%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 98.952 0.243 0.873 0.014 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 54%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.031 0.016 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 94.058 0.255 0.919 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 23.6%. 97: The balanceable part of the MD step is 34%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 8.0%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 12 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.025 0.012 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 118.087 0.203 0.732 0.016 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.5%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.028 0.014 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 103.839 0.231 0.832 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 11.7%. 97: The balanceable part of the MD step is 55%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 6.5%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 6.5 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 28 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.815 0.408 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.603 6.661 23.981 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 11.5%. 97: The balanceable part of the MD step is 69%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 8.0%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 37 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.032 0.516 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.845 8.435 30.367 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (1840 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.012 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 126.947 0.189 0.681 0.018 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 195.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 242.581 0.099 0.356 0.034 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.436 0.718 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.045 11.735 42.247 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 10 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 8 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.535 0.268 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 5.479 4.380 15.770 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 44 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.648 0.835 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.759 13.646 49.126 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 193.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 187.791 0.128 0.460 0.026 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (3122 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 143.830 0.167 0.601 0.020 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 56 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.936 0.984 196.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.493 16.076 57.875 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 196.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 244.939 0.098 0.353 0.034 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.138 0.085 162.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 17.303 1.387 4.993 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 14 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 197.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 96.198 0.249 0.898 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.069 0.040 173.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 37.122 0.647 2.327 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (2000 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.700 0.850 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.727 13.896 50.024 0.000 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.021 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 69.603 0.345 1.241 0.010 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 194.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 157.875 0.152 0.547 0.022 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 132.958 0.181 0.650 0.018 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 34 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.966 0.483 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.038 7.899 28.437 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.572 0.286 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 5.129 4.679 16.845 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (3097 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 22 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.320 0.176 181.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 8.339 2.878 10.360 0.001 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 51 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.944 0.972 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.511 15.886 57.188 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 99.129 0.242 0.872 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 19 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.033 0.017 197.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 87.735 0.274 0.985 0.012 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.028 0.014 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 103.210 0.233 0.837 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.314 0.157 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 9.349 2.567 9.242 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (2792 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.014 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 101.686 0.236 0.850 0.014 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.027 0.014 197.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 108.236 0.222 0.798 0.015 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 39 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.139 0.070 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 21.036 1.141 4.107 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.038 0.028 136.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 52.868 0.454 1.634 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.024 0.012 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 119.819 0.200 0.721 0.017 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.222 0.111 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 13.217 1.816 6.537 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1358 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 43 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.684 0.842 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.744 13.760 49.537 0.000 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 56 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.944 0.988 196.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.487 16.141 58.108 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 38 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.166 0.099 168.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 14.873 1.614 5.809 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 195.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 140.417 0.171 0.615 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.016 141.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 94.632 0.254 0.913 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (single precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 43 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.393 0.697 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.109 11.381 40.971 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (4203 ms) 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (51271 ms total) 97: 97: [----------] Global test environment tear-down 97: [==========] 25 tests from 1 test suite ran. (51287 ms total) 97: [ PASSED ] 25 tests. 97/104 Test #97: MdrunCoordinationCouplingTests2Ranks ...... Passed 51.32 sec test 98 Start 98: MdrunCoordinationConstraintsTests1Rank 98: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 98: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 98: Test timeout computed to be: 1920 98: [==========] Running 13 tests from 1 test suite. 98: [----------] Global test environment set-up. 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 164.722 0.146 0.525 0.029 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 118.432 0.203 0.730 0.021 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 115.748 0.207 0.746 0.020 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.019 0.019 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 77.435 0.310 1.116 0.013 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.015 0.015 98.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 95.801 0.251 0.902 0.017 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.016 0.016 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 89.175 0.269 0.969 0.015 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2181 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 105.528 0.227 0.819 0.018 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.005 0.009 61.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 170.871 0.140 0.506 0.030 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.009 96.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 166.395 0.144 0.519 0.029 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 98.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 207.995 0.115 0.415 0.036 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 206.302 0.116 0.419 0.036 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.016 0.016 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 89.414 0.268 0.966 0.016 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2345 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 233.347 0.103 0.370 0.041 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 106.237 0.226 0.813 0.018 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.005 0.005 99.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 275.051 0.087 0.314 0.048 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 160.625 0.149 0.538 0.028 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 116.229 0.206 0.743 0.020 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 111.389 0.215 0.776 0.019 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1646 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 135.687 0.177 0.637 0.024 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 126.735 0.189 0.682 0.022 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 195.904 0.123 0.441 0.034 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.025 0.025 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 58.825 0.408 1.469 0.010 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.005 0.005 98.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 304.558 0.079 0.284 0.053 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.017 0.017 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 87.373 0.275 0.989 0.015 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1552 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 123.916 0.194 0.697 0.022 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 158.073 0.152 0.547 0.027 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.005 0.006 91.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 255.563 0.094 0.338 0.044 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.022 0.022 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 66.246 0.362 1.304 0.012 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 192.086 0.125 0.450 0.033 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 131.825 0.182 0.655 0.023 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1433 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 165.394 0.145 0.522 0.029 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.017 0.017 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 85.345 0.281 1.012 0.015 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 121.523 0.197 0.711 0.021 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 227.765 0.105 0.379 0.040 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 166.368 0.144 0.519 0.029 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 149.228 0.161 0.579 0.026 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1944 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 173.255 0.139 0.499 0.030 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 103.426 0.232 0.835 0.018 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.016 0.016 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 89.449 0.268 0.966 0.016 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 155.378 0.154 0.556 0.027 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 156.854 0.153 0.551 0.027 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.018 0.018 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 80.081 0.300 1.079 0.014 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1505 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 113.227 0.212 0.763 0.020 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.016 0.016 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 91.708 0.262 0.942 0.016 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 180.261 0.133 0.479 0.031 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.032 0.032 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 46.455 0.517 1.860 0.008 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 98.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 216.214 0.111 0.400 0.038 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 140.714 0.171 0.614 0.024 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1596 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 140.749 0.171 0.614 0.024 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 109.850 0.218 0.787 0.019 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 222.163 0.108 0.389 0.039 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 114.206 0.210 0.757 0.020 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 161.433 0.149 0.535 0.028 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 187.737 0.128 0.460 0.033 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1758 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.019 0.019 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 77.134 0.311 1.120 0.013 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 168.982 0.142 0.511 0.029 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 131.561 0.182 0.657 0.023 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 133.682 0.180 0.646 0.023 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 199.786 0.120 0.432 0.035 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 125.310 0.192 0.689 0.022 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1369 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.015 0.015 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 94.898 0.253 0.910 0.016 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 129.153 0.186 0.669 0.022 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 118.232 0.203 0.731 0.021 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 127.641 0.188 0.677 0.022 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.028 0.028 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 52.420 0.458 1.648 0.009 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.015 0.015 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 100.283 0.239 0.862 0.017 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2021 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.053 0.053 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 27.950 0.859 3.091 0.005 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 146.590 0.164 0.589 0.025 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.023 0.023 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 64.736 0.371 1.335 0.011 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.016 0.016 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 91.074 0.264 0.949 0.016 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.017 0.017 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 86.406 0.278 1.000 0.015 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.018 0.018 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 82.991 0.289 1.041 0.014 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2083 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 217.812 0.110 0.397 0.038 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 109.302 0.220 0.790 0.019 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 101.610 0.236 0.850 0.018 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.031 0.031 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 47.975 0.500 1.801 0.008 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 124.640 0.193 0.693 0.022 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 121.300 0.198 0.712 0.021 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1812 ms) 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (23249 ms total) 98: 98: [----------] Global test environment tear-down 98: [==========] 13 tests from 1 test suite ran. (23260 ms total) 98: [ PASSED ] 13 tests. 98/104 Test #98: MdrunCoordinationConstraintsTests1Rank .... Passed 23.30 sec test 99 Start 99: MdrunCoordinationConstraintsTests2Ranks 99: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 99: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 99: Test timeout computed to be: 1920 99: [==========] Running 13 tests from 1 test suite. 99: [----------] Global test environment set-up. 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.8%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 55 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.029 0.015 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 100.834 0.238 0.857 0.018 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.1%. 99: The balanceable part of the MD step is 42%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 48 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.030 0.015 199.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 96.326 0.249 0.897 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.2%. 99: The balanceable part of the MD step is 37%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: NOTE: 49 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.036 0.018 199.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 80.884 0.297 1.068 0.014 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.2%. 99: The balanceable part of the MD step is 25%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 25 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 36 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 111.069 0.216 0.778 0.019 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.7%. 99: The balanceable part of the MD step is 33%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 51 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.317 0.159 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 9.251 2.594 9.339 0.002 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.1%. 99: The balanceable part of the MD step is 33%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: NOTE: 50 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.511 0.255 200.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 5.752 4.173 15.022 0.001 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2855 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.0%. 99: The balanceable part of the MD step is 27%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 40 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.761 0.380 200.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 3.861 6.215 22.375 0.001 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 54 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.046 0.023 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 63.123 0.380 1.369 0.011 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.4%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 52 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.046 0.023 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 64.164 0.374 1.347 0.011 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.5%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 49 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.068 0.034 199.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 42.962 0.559 2.011 0.007 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.5%. 99: The balanceable part of the MD step is 36%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 50 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.178 0.089 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 16.443 1.460 5.254 0.003 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.6%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 48 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.021 0.011 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 136.104 0.176 0.635 0.024 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4112 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.6%. 99: The balanceable part of the MD step is 0%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 40 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 11 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.161 0.081 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 18.228 1.317 4.740 0.003 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.8%. 99: The balanceable part of the MD step is 43%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 197.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 228.742 0.105 0.378 0.040 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.5%. 99: The balanceable part of the MD step is 40%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 49 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.032 0.016 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 90.338 0.266 0.956 0.016 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.7%. 99: The balanceable part of the MD step is 38%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 63 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 217.874 0.110 0.397 0.038 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.1%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 61 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.031 0.016 197.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 94.103 0.255 0.918 0.016 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.4%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 58 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.007 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 198.758 0.121 0.435 0.035 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3323 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.023 0.012 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 124.932 0.192 0.692 0.022 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.028 0.014 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 105.171 0.228 0.822 0.018 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 148.781 0.161 0.581 0.026 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.029 0.015 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 99.137 0.242 0.872 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.051 0.026 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 57.248 0.419 1.509 0.010 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.079 0.039 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 37.224 0.645 2.321 0.006 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3519 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.047 0.024 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 62.055 0.387 1.392 0.011 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.119 0.060 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 24.644 0.974 3.506 0.004 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.023 0.011 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 129.460 0.185 0.667 0.022 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 177.225 0.135 0.488 0.031 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 240.945 0.100 0.359 0.042 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 193.422 0.124 0.447 0.034 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3252 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.028 0.014 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 105.067 0.228 0.822 0.018 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.029 0.015 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 99.671 0.241 0.867 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 16 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 33 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.784 0.408 192.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 3.602 6.663 23.988 0.001 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.037 0.018 199.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 79.644 0.301 1.085 0.014 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.070 0.035 199.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 41.972 0.572 2.059 0.007 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.525 0.263 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 5.590 4.294 15.457 0.001 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3930 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 23 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.516 0.758 200.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.937 12.389 44.602 0.000 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.066 0.033 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 44.221 0.543 1.954 0.008 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.114 0.057 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 25.713 0.933 3.360 0.004 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 10 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.488 0.760 195.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.933 12.416 44.698 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 190.914 0.126 0.453 0.033 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 216.556 0.111 0.399 0.038 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4809 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 27 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.265 0.133 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 11.077 2.167 7.800 0.002 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.023 0.012 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 126.713 0.189 0.682 0.022 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 69 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.052 0.026 199.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 56.008 0.429 1.543 0.010 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 28 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.904 0.968 196.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.517 15.816 56.938 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 29 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.872 0.952 196.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.543 15.553 55.991 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 213.865 0.112 0.404 0.037 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (6176 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.031 0.016 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 93.149 0.258 0.928 0.016 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 32 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.075 0.053 140.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 27.503 0.873 3.141 0.005 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 220.889 0.109 0.391 0.038 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 35 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.069 0.051 136.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 29.071 0.826 2.972 0.005 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 36 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.067 0.050 135.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 29.669 0.809 2.912 0.005 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.012 0.006 198.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 241.905 0.099 0.357 0.042 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3428 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 10.9%. 99: The balanceable part of the MD step is 3%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.046 0.025 183.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 58.874 0.408 1.468 0.010 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.8%. 99: The balanceable part of the MD step is 55%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 196.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 224.581 0.107 0.385 0.039 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.7%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 113.021 0.212 0.764 0.020 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.0%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 12 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 18 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.712 0.872 196.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.685 14.246 51.285 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.5%. 99: The balanceable part of the MD step is 43%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 40 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.138 0.085 162.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 17.310 1.386 4.991 0.003 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.8%. 99: The balanceable part of the MD step is 0%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 10 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 10 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.631 0.316 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 4.655 5.155 18.559 0.001 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (4017 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.2%. 99: The balanceable part of the MD step is 54%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.1%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 197.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 147.006 0.163 0.588 0.026 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.9%. 99: The balanceable part of the MD step is 50%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.049 0.025 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 59.075 0.406 1.463 0.010 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.9%. 99: The balanceable part of the MD step is 50%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.031 0.016 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 93.189 0.258 0.927 0.016 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.7%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 112.507 0.213 0.768 0.020 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.6%. 99: The balanceable part of the MD step is 43%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.481 0.241 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 6.104 3.932 14.155 0.001 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.7%. 99: The balanceable part of the MD step is 50%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 195.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 145.975 0.164 0.592 0.025 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2834 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.072 0.036 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 40.609 0.591 2.128 0.007 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.054 0.027 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 53.649 0.447 1.610 0.009 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.080 0.040 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 36.504 0.657 2.367 0.006 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.030 0.015 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 96.177 0.250 0.898 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 196.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 188.389 0.127 0.459 0.033 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.093 0.047 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 31.477 0.762 2.745 0.005 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3907 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 195.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 221.552 0.108 0.390 0.038 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 196.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 163.402 0.147 0.529 0.028 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.204 0.102 199.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 14.377 1.669 6.010 0.002 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.072 0.036 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 40.861 0.587 2.114 0.007 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.038 0.019 197.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 75.788 0.317 1.140 0.013 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 40 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 3.902 1.951 200.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 0.753 31.880 114.768 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (5034 ms) 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (51202 ms total) 99: 99: [----------] Global test environment tear-down 99: [==========] 13 tests from 1 test suite ran. (51224 ms total) 99: [ PASSED ] 13 tests. 99/104 Test #99: MdrunCoordinationConstraintsTests2Ranks ... Passed 51.25 sec test 100 Start 100: MdrunFEPTests 100: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunFEPTests.xml" 100: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 100: Test timeout computed to be: 600 100: [==========] Running 14 tests from 2 test suites. 100: [----------] Global test environment set-up. 100: [----------] 2 tests from ExpandedEnsembleTest 100: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 16 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.043 0.022 199.5 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 68.193 0.352 1.267 0.028 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 100: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 100: 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.238 0.119 199.9 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 6.526 3.678 13.240 0.003 100: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (198 ms) 100: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 1 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.082 0.041 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 4.223 5.684 20.462 0.002 100: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (74 ms) 100: [----------] 2 tests from ExpandedEnsembleTest (272 ms total) 100: 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -1652834313 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.077 0.539 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 3.368 7.126 25.653 0.007 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (43984 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 2129379326 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.090 0.545 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 3.328 7.212 25.964 0.007 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (737 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -1107452417 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.129 0.564 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 3.215 7.465 26.873 0.007 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (749 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 155]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 155]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to 1790435069 100: 100: Generated 171 of the 171 non-bonded parameter combinations 100: 100: Generated 171 of the 171 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 358.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 1 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.96 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.711 0.356 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 5.102 4.704 16.934 0.011 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (49360 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 165]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 165]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to -1678114833 100: 100: Generated 190 of the 190 non-bonded parameter combinations 100: 100: Generated 190 of the 190 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'CL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'CL' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 361.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 2 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.96 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.757 0.378 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 4.794 5.006 18.022 0.010 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (452 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 100: and vdw_modifier=Force-switch 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 100 steps, 0.1 ps. 100: Setting the LD random seed to -337667205 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.531 0.266 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 32.863 0.730 2.629 0.067 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (428 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There were 11 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -4718913 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.95 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.088 0.544 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 3.336 7.194 25.898 0.007 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (687 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: Removing center of mass motion in the presence of position restraints 100: might cause artifacts. When you are using position restraints to 100: equilibrate a macro-molecule, the artifacts are usually negligible. 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There were 11 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 1004437495 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.94 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.075 0.538 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 3.374 7.113 25.607 0.007 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (670 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 2142894453 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.89 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.499 0.250 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 7.266 3.303 11.891 0.015 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (420 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: There was 1 NOTE 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.048 0.024 199.2 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 75.807 0.317 1.140 0.155 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -537938058 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.90 100: 100: This run will generate roughly 0 Mb of data 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (132 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -309334109 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.95 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.557 0.278 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 6.516 3.683 13.260 0.013 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (427 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2026.3-Debian_1 (single precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 2042620863 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.90 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.061 0.031 199.6 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 59.134 0.406 1.461 0.121 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (116 ms) 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (98171 ms total) 100: 100: [----------] Global test environment tear-down 100: [==========] 14 tests from 2 test suites ran. (98491 ms total) 100: [ PASSED ] 14 tests. 100/104 Test #100: MdrunFEPTests ............................. Passed 98.53 sec test 101 Start 101: MdrunPullTests 101: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunPullTests.xml" 101: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 101: Test timeout computed to be: 600 101: [==========] Running 4 tests from 1 test suite. 101: [----------] Global test environment set-up. 101: [----------] 4 tests from PullTest/PullIntegrationTest 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.600 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.063 0.032 199.7 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 57.596 0.417 1.500 0.432 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (464 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.301 nm 0.400 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.207 0.103 199.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 17.544 1.368 4.925 0.132 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (563 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Pull group 3 'r_3' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1292.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.357 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.500 nm 101: 1 3 2 101: 3 3 8 0.331 nm 0.400 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.251 0.125 199.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 14.469 1.659 5.971 0.109 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (551 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.000 nm 101: 0.050 nm 0.000 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.960 0.480 200.0 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 3.778 6.352 22.868 0.028 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (920 ms) 101: [----------] 4 tests from PullTest/PullIntegrationTest (2501 ms total) 101: 101: [----------] Global test environment tear-down 101: [==========] 4 tests from 1 test suite ran. (2517 ms total) 101: [ PASSED ] 4 tests. 101/104 Test #101: MdrunPullTests ............................ Passed 2.55 sec test 102 Start 102: MdrunRotationTests 102: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunRotationTests.xml" 102: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 102: Test timeout computed to be: 600 102: [==========] Running 12 tests from 1 test suite. 102: [----------] Global test environment set-up. 102: [----------] 12 tests from RotationWorks/RotationTest 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 102: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: trr version: GMX_trn_file (single precision) 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -4325446 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.025 0.012 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 360.447 0.067 0.479 0.008 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (40 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 102: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -134397957 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 369.718 0.065 0.467 0.009 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (29 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 102: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 1543466747 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 372.069 0.065 0.464 0.009 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (27 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 102: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -152107026 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.009 198.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 478.424 0.050 0.361 0.011 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (15 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 102: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -268771346 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.033 0.017 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 267.608 0.090 0.646 0.006 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (26 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 102: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -6560258 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: NOTE: 17 % of the run time was spent in pair search, 102: you might want to increase nstlist (this has no effect on accuracy) 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.206 0.103 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 43.592 0.551 3.964 0.001 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (133 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 102: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -5285 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.010 198.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 460.445 0.052 0.375 0.011 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (20 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 102: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -146808842 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.027 0.014 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 329.738 0.073 0.524 0.008 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (19 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 102: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 1474160509 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.030 0.015 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 294.197 0.082 0.587 0.007 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (29 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 102: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -72647538 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.036 0.018 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 246.726 0.097 0.700 0.006 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (28 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 102: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -268984993 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.052 0.026 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 172.822 0.139 1.000 0.004 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (38 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 102: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2026.3-Debian_1 (single precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 1609023419 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: NOTE: 10 % of the run time was spent in pair search, 102: you might want to increase nstlist (this has no effect on accuracy) 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.321 0.161 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.980 0.858 6.176 0.001 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (177 ms) 102: [----------] 12 tests from RotationWorks/RotationTest (590 ms total) 102: 102: [----------] Global test environment tear-down 102: [==========] 12 tests from 1 test suite ran. (606 ms total) 102: [ PASSED ] 12 tests. 102/104 Test #102: MdrunRotationTests ........................ Passed 0.64 sec test 103 Start 103: MdrunSimulatorComparison 103: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 103: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 103: Test timeout computed to be: 600 103: [==========] Running 0 tests from 0 test suites. 103: [==========] 0 tests from 0 test suites ran. (0 ms total) 103: [ PASSED ] 0 tests. 103: 103: YOU HAVE 82 DISABLED TESTS 103: 103/104 Test #103: MdrunSimulatorComparison .................. Passed 0.03 sec test 104 Start 104: MdrunVirtualSiteTests 104: Test command: /build/reproducible-path/gromacs-2026.3/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 104: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests 104: Test timeout computed to be: 600 104: [==========] Running 37 tests from 2 test suites. 104: [----------] Global test environment set-up. 104: [----------] 1 test from VirtualSiteVelocityTest 104: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 104: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 104: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 104: 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 1.1%. 104: The balanceable part of the MD step is 40%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.5%. 104: 104: 104: NOTE: 54 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.029 0.014 199.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 54.168 0.443 1.595 0.015 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.3-Debian_1 (single precision) 104: trr version: GMX_trn_file (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (47 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 1.7%. 104: The balanceable part of the MD step is 34%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.6%. 104: 104: 104: NOTE: 91 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.062 0.055 113.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 14.115 1.700 6.121 0.004 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (259 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 1.1%. 104: The balanceable part of the MD step is 35%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.4%. 104: 104: 104: NOTE: 75 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.039 0.036 110.3 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 21.886 1.097 3.948 0.006 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (144 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 17 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.048 0.040 119.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 19.547 1.228 4.420 0.005 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (168 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 77 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.056 0.052 108.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 14.924 1.608 5.789 0.004 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (163 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 49 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.021 0.010 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 74.685 0.321 1.157 0.021 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (221 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 16 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 8 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.822 0.411 200.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.891 12.692 45.691 0.001 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (704 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 51 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.126 0.063 199.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 12.290 1.953 7.030 0.003 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (526 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 55 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.029 0.014 199.1 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 54.010 0.444 1.600 0.015 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (324 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 1.7%. 104: The balanceable part of the MD step is 36%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.6%. 104: 104: 104: NOTE: 72 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.042 0.037 114.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 20.953 1.145 4.123 0.006 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (160 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 11.4%. 104: The balanceable part of the MD step is 34%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 3.9%. 104: 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.042 0.021 199.4 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 36.513 0.657 2.366 0.010 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (588 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 51 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.021 0.011 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 73.995 0.324 1.168 0.021 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (34 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.019 0.009 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 83.008 0.289 1.041 0.023 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (35 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 12 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 25 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 1.080 0.556 194.3 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.399 17.155 61.757 0.000 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (1288 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.020 0.010 198.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 78.376 0.306 1.102 0.022 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (263 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 50 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 11 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.056 0.028 199.6 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 27.729 0.866 3.116 0.008 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (447 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 15 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 10 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.848 0.440 192.7 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.768 13.575 48.868 0.000 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (1131 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 49 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.025 0.012 199.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 63.005 0.381 1.371 0.018 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (64 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 34 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 16 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.372 0.202 184.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 3.853 6.228 22.422 0.001 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (695 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.016 0.008 198.7 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 99.457 0.241 0.869 0.028 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (192 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.018 0.009 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 84.538 0.284 1.022 0.023 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.3-Debian_1 (single precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.3-Debian_1 (single precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (83 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (7548 ms total) 104: 104: [----------] Global test environment tear-down 104: [==========] 37 tests from 2 test suites ran. (7564 ms total) 104: [ PASSED ] 37 tests. 104/104 Test #104: MdrunVirtualSiteTests ..................... Passed 7.60 sec 100% tests passed, 0 tests failed out of 104 Label Time Summary: GTest = 3141.19 sec*proc (97 tests) IntegrationTest = 2875.08 sec*proc (30 tests) MpiTest = 2520.69 sec*proc (24 tests) QuickGpuTest = 178.95 sec*proc (25 tests) SlowGpuTest = 2936.77 sec*proc (15 tests) SlowTest = 249.68 sec*proc (14 tests) UnitTest = 16.44 sec*proc (53 tests) Total Test time (real) = 1127.40 sec /usr/bin/make -j8 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.3 -B/build/reproducible-path/gromacs-2026.3/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.3 -B/build/reproducible-path/gromacs-2026.3/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E 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'/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/DependInfo.cmake "--color=" mpithreads /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fmm/CMakeFiles/fmm.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/DependInfo.cmake "--color=" sync_cyclecount make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 3%] Built target linearalgebra [ 4%] Built target fmm /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/DependInfo.cmake "--color=" mpi_speedtest [ 5%] Built target options /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -MF CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o.d -o CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/sync_cyclecount.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 5%] Built target h5md /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build.make src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/depend /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/notmpi.dir/DependInfo.cmake "--color=" notmpi make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/DependInfo.cmake "--color=" alloc_check make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -MF CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/mpi_speedtest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/notmpi.dir/notmpi.cpp.o -MF CMakeFiles/notmpi.dir/notmpi.cpp.o.d -o CMakeFiles/notmpi.dir/notmpi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/notmpi.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f 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/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/alloc_check.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 5%] Built target pulling cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/send_recv.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/alloc_check.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/sync_cyclecount.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -MF CMakeFiles/mpi_speedtest.dir/multicast.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/multicast.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sync_cyclecount.dir/link.d CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/sync_cyclecount /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alloc_check.dir/link.d CMakeFiles/alloc_check.dir/alloc_check.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/alloc_check make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 7%] Built target alloc_check /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 7%] Built target sync_cyclecount /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/multicast.cpp.o -MF CMakeFiles/mpithreads.dir/multicast.cpp.o.d -o CMakeFiles/mpithreads.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/multicast.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cond-var.cpp.o -MF CMakeFiles/mpithreads.dir/cond-var.cpp.o.d -o CMakeFiles/mpithreads.dir/cond-var.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/cond-var.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 7%] Built target energyanalysis /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend [ 7%] Built target taskassignment make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/atomic.cpp.o -MF CMakeFiles/mpithreads.dir/atomic.cpp.o.d -o CMakeFiles/mpithreads.dir/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/atomic.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cycles.cpp.o -MF CMakeFiles/mpithreads.dir/cycles.cpp.o.d -o CMakeFiles/mpithreads.dir/cycles.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/cycles.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/notmpi.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/split.cpp.o -MF CMakeFiles/mpithreads.dir/split.cpp.o.d -o CMakeFiles/mpithreads.dir/split.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/test/split.cpp [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/notmpi.dir/link.d CMakeFiles/notmpi.dir/notmpi.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/notmpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 8%] Built target notmpi cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpi_speedtest.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/mpithreads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpi_speedtest.dir/link.d CMakeFiles/mpi_speedtest.dir/mpi_speedtest.cpp.o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o 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'/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/googletest/googlemock /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" gmock make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wundef -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF 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/usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/posixmemstream.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/setenv.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o 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'/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake "--color=" utility-test make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake "--color=" nblib_test_infrastructure make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" mdlib-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/energyreader.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/mpicomm.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/testsystems.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/tests/interactivetest.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o -MF CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/coordinate_exception_handling.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/tests/naming.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 62%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constr.cpp /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/moduletest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpicomm-test.dir/link.d "CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o" "CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mpicomm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 62%] Built target mpicomm-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/bias.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o" "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 62%] Built target utility-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem 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CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include 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src/testutils/tests/CMakeFiles/testutils-test.dir/posixmemstream.cpp.o -MF CMakeFiles/testutils-test.dir/posixmemstream.cpp.o.d -o CMakeFiles/testutils-test.dir/posixmemstream.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/tests/posixmemstream.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 62%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -MF CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o.d -o CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constraintgroupsize.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/booltype.cpp /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" density_fitting_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" 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-isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem 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CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/bitmask32.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/posixmemstream.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 64%] Built target testutils-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" qmmm_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 64%] Built target density_fitting_applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmforceproviderstate.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" colvars_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 64%] Built target awh-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" plumed_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 64%] Built target plumed_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" plumed_md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" nnpot_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/parrinellorahman.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 65%] Built target qmmm_applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 66%] Built target plumed_md-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 67%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" listed_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 67%] Built target applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/listed_forces/tests/position_restraints.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" nbnxm-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" nbnxm-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/pairlist.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 67%] Built target nnpot_applied_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 68%] Built target nbnxm-gpu-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mpicomm.cpp.o -MF CMakeFiles/utility-test.dir/mpicomm.cpp.o.d -o CMakeFiles/utility-test.dir/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 68%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -MF CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o.d -o CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/plainpairlist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" nonbonded-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/vsite.cpp.o -MF CMakeFiles/mdlib-test.dir/vsite.cpp.o.d -o CMakeFiles/mdlib-test.dir/vsite.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/vsite.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/DependInfo.cmake "--color=" nonbonded-fep-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/freeenergygpukernel.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/testsystem.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-gpu-test.dir/link.d "CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o" "CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 69%] Built target nonbonded-fep-gpu-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/testsystem.cpp: In function ‘std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)’: /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/template_mp.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" onlinehelp-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests/mock_helptopic.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 69%] Built target nbnxm-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/textwriter.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" domdec-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" domdec-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 69%] Built target onlinehelp-test-shared cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/txtdump.cpp.o -MF CMakeFiles/utility-test.dir/txtdump.cpp.o.d -o CMakeFiles/utility-test.dir/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/txtdump.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 69%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests 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'/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmegathertest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/vsite.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 71%] Built target mdlib-test /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/DependInfo.cmake "--color=" fmm-interface-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests/fmm_mdpoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 71%] Built target domdec-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 71%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vecdump.cpp.o -MF CMakeFiles/utility-test.dir/vecdump.cpp.o.d -o CMakeFiles/utility-test.dir/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/vecdump.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests/fmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/tests/fmmforceproviderbuilder.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 71%] Built target fft-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vectypes.cpp.o -MF CMakeFiles/utility-test.dir/vectypes.cpp.o.d -o CMakeFiles/utility-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/utility/tests/vectypes.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/device_availability.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/DependInfo.cmake "--color=" gpu_utils-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o -MF CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o.d -o CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fmm-interface-tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fmm-interface-tests.dir/link.d "CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o" "CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fmm-interface-tests ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 71%] Built target fmm-interface-tests cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include 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/build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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-f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include 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src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 71%] Built target ewald-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" 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-I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-mpi-test.dir/link.d "CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o" "CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 75%] Built target gpu_utils-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/complex.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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'/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include 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CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 75%] Built target hardware-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 75%] Built target onlinehelp-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/exponentialmovingaverage.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/exponentialdistribution.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 75%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 75%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 76%] Built target mdspan-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 77%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF 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'/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/tests/inmemoryserializer.cpp /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" taskassignment-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 77%] Built target mdtypes-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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/build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/invertmatrix.cpp /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" timing-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/serialization-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 78%] Built target taskassignment-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/serialization-test.dir/link.d "CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/serialization-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 79%] Built target serialization-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 79%] Built target random-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 80%] Built target timing-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 80%] Built target table-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/neldermead.cpp /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 80%] Built target pull-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/bootstrap_loadstore.cpp /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/generate_test_points.cpp.o -MF CMakeFiles/simd-test.dir/generate_test_points.cpp.o.d -o CMakeFiles/simd-test.dir/generate_test_points.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/generate_test_points.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/compat/tests/pointers.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -MF CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmxanatestbase.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/index.cpp /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/generate_test_points.cpp: In function ‘std::vector gmx::test::generateTestPoints(RealRange, std::size_t)’: /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/generate_test_points.cpp:53:19: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 53 | std::vector generateTestPoints(RealRange inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 80%] Built target compat-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_rms.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_rmsf.cpp cd 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-o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/genconf.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxana/tests/gmx_traj.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 81%] Built target topology-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 81%] Built target options-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 82%] Built target gmxana-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 82%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" correlations-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include 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/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" analysisdata-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make 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'/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 82%] Built target pdb2gmx3-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/readir.cpp /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_memory.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 83%] Built target math-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 83%] Built target correlations-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" tool-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 84%] Built target energyanalysis-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/register.cpp /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_math.cpp: In static member function ‘static void gmx::test::SimdMathTest::generateTestPointsTest()’: /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd_math.cpp:309:32: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 309 | result = generateTestPoints({ -1e10, -1 }, points); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 84%] Built target analysisdata-test-shared cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/trjconv.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 85%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4_math.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" tool-test-with-leaks make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/tools/tests/convert-tpr.cpp /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/DependInfo.cmake "--color=" h5md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/h5md/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/generate_test_points.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 86%] Built target simd-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" fileio-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/setbothtime.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 86%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/h5md-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/h5md-test.dir/link.d "CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o" "CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/h5md.dir/h5md.cpp.o -o ../../../../../bin/h5md-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 87%] Built target h5md-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" mdrun-output-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/nbsearch.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 87%] Built target tool-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem 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CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/filetypes.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" 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/build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 88%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/selectionoption.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 89%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 89%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" 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/build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem 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CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/readinp.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/awh.cpp.o -MF CMakeFiles/mdrun-test.dir/awh.cpp.o.d -o CMakeFiles/mdrun-test.dir/awh.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/awh.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" mdrun-single-rank-algorithms-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/dispersion_correction.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" minimize-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/tests/timecontrol.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 89%] Built target selection-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/initialconstraints.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 89%] Built target minimize-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/freezegroups.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 89%] Built target mdrun-single-rank-algorithms-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/termination.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/rerun.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" mdrun-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 89%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/boxdeformation.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 90%] Built target fileio-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" mdrun-multisim-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 90%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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/build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-equivalence-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 90%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" mdrun-mpi-pme-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" mdrun-coordination-basic-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include 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/build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 90%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions_basic.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/awh.cpp.o" "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 91%] Built target mdrun-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 92%] Built target mdrun-multisim-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 92%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" mdrun-coordination-constraints-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" mdrun-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/expandedensemble.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 92%] Built target mdrun-mpi-pme-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/freeenergy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 93%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" mdrun-pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" mdrun-rotation-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 93%] Built target mdrun-coordination-basic-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" mdrun-simulator-comparison-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 93%] Built target mdrun-multisim-replex-equivalence-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" mdrun-vsites-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/tests/virtualsites.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external 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cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" gmxapi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make 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-I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" workflow-details-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/workflow/tests/workflow.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" nblib-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 93%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" nblib-setup-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 94%] Built target workflow-details-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 94%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" nblib-tpr-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 94%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/system.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 95%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 95%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 96%] Built target nblib-integrator-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" nblib-integration-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/topology.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 96%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.3/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" nblib-listed-forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd 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-I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib/util/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" nblib-util-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 96%] Built target gmxapi-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -MF CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/plainpairlistranges.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 96%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 96%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" analysisdata-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 97%] Built target nblib-setup-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 97%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.3/api/nblib/listed_forces/tests/transformations.cpp /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" nblib-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/nblib/tests -I/build/reproducible-path/gromacs-2026.3/api/nblib/include -I/build/reproducible-path/gromacs-2026.3/api/nblib -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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"CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 97%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/rdf.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 98%] Built target commandline-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/testutils/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -isystem /build/reproducible-path/gromacs-2026.3/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.3/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' cd /build/reproducible-path/gromacs-2026.3/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp /build/reproducible-path/gromacs-2026.3/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.3/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.3/build/basic-dp/lib ctest -V ) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2026.3/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2026.3/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2026.3/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -339755019 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.058 0.029 199.5 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 17.277 1.389 9.767 0.001 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (638 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1661671633 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.060 0.030 199.6 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 16.873 1.422 10.001 0.001 1: [ OK ] GmxApiTest.RunnerBasicMD (650 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -268650019 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.223 0.112 199.9 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 31.764 0.756 5.313 0.002 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.024 0.012 198.7 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 292.555 0.082 0.577 0.014 1: [ OK ] GmxApiTest.RunnerReinitialize (734 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 2013228590 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.027 0.013 198.9 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 37.917 0.633 4.451 0.002 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: NOTE: 10 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.062 0.031 199.7 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 16.340 1.469 10.328 0.001 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (420 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to 1941962495 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 21 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.117 0.058 199.8 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 14.466 1.659 11.665 0.001 1: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.3-Debian_1 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 29 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.050 0.025 199.4 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 13.566 1.769 12.439 0.001 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (469 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -76677133 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (358 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (3273 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (3292 ms total) 1: [ PASSED ] 9 tests. 1/104 Test #1: GmxapiExternalInterfaceTests .............. Passed 3.39 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -1073742881 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (452 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -438829193 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (337 ms) 2: [----------] 2 tests from GmxApiTest (794 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (810 ms total) 2: [ PASSED ] 2 tests. 2/104 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.84 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (6 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (1 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (21 ms) 3: [----------] 8 tests from NBlibTest (34 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (1 ms) 3: [----------] 7 tests from ThreeCenter (5 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (3 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (1 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (7 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (2 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (6 ms) 3: [----------] 1 test from LinearChainDataFixture (6 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (56 ms total) 3: [ PASSED ] 44 tests. 3/104 Test #3: NbLibListedForcesTests .................... Passed 0.09 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/104 Test #4: NbLibSamplesTestArgon ..................... Passed 0.03 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/104 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.06 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 60 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/104 Test #6: NbLibUtilTests ............................ Passed 0.03 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (1 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (1 ms total) 7: [ PASSED ] 57 tests. 7/104 Test #7: NbLibSetupTests ........................... Passed 0.05 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 60 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2026.3-Debian_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (17 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2026.3-Debian_1 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (14 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2026.3-Debian_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (6 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (12 ms) 8: [----------] 4 tests from TprReaderTest (59 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (74 ms total) 8: [ PASSED ] 4 tests. 8/104 Test #8: NbLibTprTests ............................. Passed 0.11 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (1 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (2 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (3 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (16 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (22 ms total) 9: [ PASSED ] 20 tests. 9/104 Test #9: NbLibIntegrationTests ..................... Passed 0.05 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/104 Test #10: NbLibIntegratorTests ...................... Passed 0.03 sec test 11 Start 11: threadMPI-mpithreads 11: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mpithreads "-nt" "3" 11: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test 11: Test timeout computed to be: 1500 11: 11: thread_mpi tester. 11: 11: Number of threads: 3 11: 11: thread 2: got arg 10; total number of hw threads: 12 11: my rank = 2 11: thread 1: got arg 10; total number of hw threads: 12 11: my rank = 1 11: thread 0: got arg 10; total number of hw threads: 12 11: my rank = 0 11: Setting thread affinity 11: Testing atomic functions.. 11: OK. 11: Starting tMPI_Thread_cond_signal test: 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 1: 457 11: processed by thread 2: 543 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 521 11: processed by thread 2: 479 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 670 11: processed by thread 1: 330 11: 11: Starting tMPI_Thread_cond_broadcast test: 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 1: 228 11: processed by thread 2: 1772 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 2000 11: processed by thread 2: 0 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 669 11: processed by thread 1: 1331 11: 11: 11: sizeof(atomic_t) = 4, sizeof(atomic_t_ptr)=8, sizeof(spinlock)=4 11: Testing spinlocks.. 11: OK. 11: 11: Testing locks.. 11: OK. 11: 11: Barrier data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Starting MPI_Send and MPI_Recv tests 11: Received: 'From thread 1 to 0: hello.' 11: Received: 'From thread 2 to 0: hello.' 11: Received: 'From thread 1 to 1: hello.' 11: Received: 'From thread 2 to 1: hello.' 11: 11: Starting MPI_Sendrecv tests 11: Received: 'Sendrecv hello, from thread 1' 11: Received: 'Sendrecv hello, from thread 2' 11: Received: 'Sendrecv hello, from thread 0' 11: 11: Starting MPI_Isend/MPI_Irecv tests 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Split test 11: I'm in world rank 0, and have new rank 1 in group 0xaaaada1a11f0 of size 2 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0xaaaada1a11f0 of size 2 11: I'm in world rank 1, and have new rank 0 in group 0xaaaada1a1760 of size 1 11: I'm in world rank 0, and have new rank 0 in group 0xaaaada1a1bb0 of size 1 11: my rank is 0, MPI_Comm_compare said: 3 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0xaaaada1a2190 of size 1 11: my rank is 2, MPI_Comm_compare said: 3 11: I'm in world rank 1, and have new rank 0 in group 0xaaaada1a1e30 of size 1 11: my rank is 1, MPI_Comm_compare said: 3 11: I'm in world rank 0, and have new rank 2 in group 0xaaaada1a1bb0 of size 3 11: my rank is 0, MPI_Comm_compare said: 2 11: Starting repeated MPI_Split() test. 11: I'm in world rank 2, and have new rank 0 in group 0xaaaada1a1bb0 of size 3 11: my rank is 2, MPI_Comm_compare said: 2 11: I'm in world rank 1, and have new rank 1 in group 0xaaaada1a1bb0 of size 3 11: my rank is 1, MPI_Comm_compare said: 2 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: Done. 11: 11: Starting MPI_Bcast test 11: Received: 'Broadcast message 0 from 0' 11: Received: 'Broadcast message 0 from 1' 11: Received: 'Broadcast message 0 from 2' 11: Received: 'Broadcast message 1 from 0' 11: Received: 'Broadcast message 1 from 1' 11: Received: 'Broadcast message 1 from 2' 11: Broadcast data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Gather test 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Gather data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Gatherv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Scatter test 11: Received from 0: 'Scatter message from 000 to 000' 11: Received back from 1: 'Scatter message from 000 to 001' 11: Received back from 2: 'Scatter message from 000 to 002' 11: Scatter data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Scatterv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Alltoall test 11: From 0: 0->0(0) 1->0(0) 2->0(0) 11: From 1: 0->1(0) 1->1(0) 2->1(0) 11: From 2: 0->2(0) 1->2(0) 2->2(0) 11: From 0: 0->0(1) 1->0(1) 2->0(1) 11: From 1: 0->1(1) 1->1(1) 2->1(1) 11: From 2: 0->2(1) 1->2(1) 2->2(1) 11: From 0: 0->0(2) 1->0(2) 2->0(2) 11: From 1: 0->1(2) 1->1(2) 2->1(2) 11: From 2: 0->2(2) 1->2(2) 2->2(2) 11: From 0: 0->0(3) 1->0(3) 2->0(3) 11: From 1: 0->1(3) 1->1(3) 2->1(3) 11: From 2: 0->2(3) 1->2(3) 2->2(3) 11: Alltoallv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Reduce test 11: again: my rank = 0 11: Results from mpi_reduce: 11: (0: 2 == 2): OK 11: (1: 5 == 5): OK 11: (2: 8 == 8): OK 11: (3: 11 == 11): OK 11: (4: 14 == 14): OK 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 1 11: again: my rank = 2 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 1: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 2: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: again: my rank = 1 11: again: my rank = 0 11: again: my rank = 2 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 1: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 2: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 2 11: again: my rank = 1 11: again: my rank = 0 11: 11: Starting tMPI_Scan test 11: Results from mpi_scan process 0: 11: OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Once test 11: Printing this number once: 0 (my rank=2) 11: Printing this number once: 2 (my rank=1) 11: I was first for 0, my rank=2 11: Printing this number once: 3 (my rank=1) 11: Printing this number once: 4 (my rank=1) 11: Printing this number once: 5 (my rank=1) 11: Printing this number once: 6 (my rank=1) 11: Printing this number once: 7 (my rank=1) 11: Printing this number once: 8 (my rank=1) 11: Printing this number once: 9 (my rank=1) 11: Printing this number once: 1 (my rank=0) 11: Done. 11: 11: Finishing.. 11/104 Test #11: threadMPI-mpithreads ...................... Passed 43.13 sec test 12 Start 12: threadMPI-sync_cyclecount 12: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/sync_cyclecount "2" "0" "1" 12: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test 12: Test timeout computed to be: 1500 12: 12: sync_cyclecount. 12: 12: Number of threads: 3 12: 12: Number of counters: 3 12: 12: No cycle count. 12/104 Test #12: threadMPI-sync_cyclecount ................. Passed 0.01 sec test 13 Start 13: threadMPI-mpi_speedtest 13: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mpi_speedtest "-nt" "3" 13: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test 13: Test timeout computed to be: 1500 13: No cycle count. 13: No cycle count. 13: No cycle count. 13/104 Test #13: threadMPI-mpi_speedtest ................... Passed 0.01 sec test 14 Start 14: threadMPI-notmpi 14: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/notmpi "-nt" "3" 14: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test 14: Test timeout computed to be: 1500 14: 14: notmpi. 14: 14: Number of threads: 3 14: 14: This platform supports setting thread affinity 14: My ID=1, i=1000, tid=0xffff7c000be0 14: My ID=0, i=1000, tid=0xaaaabee275f0 14: My ID=2, i=1000, tid=0xffff7c000be0 14: Total count: 3000 14/104 Test #14: threadMPI-notmpi .......................... Passed 0.01 sec test 15 Start 15: threadMPI-alloc_check 15: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/alloc_check "-nt" "3" 15: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/external/thread_mpi/test 15: Test timeout computed to be: 1500 15: 15: Memory (de)allocation tester. 15: 15: Number of threads: 3 15: 15: thread 1: got arg 10; total number of hw threads: 12 15: my rank = 1 15: thread 0: got arg 10; total number of hw threads: 12 15: my rank = 0 15: thread 2: got arg 10; total number of hw threads: 12 15: my rank = 2 15: 15: Starting MPI_Sendrecv tests 15: Received: 'Sendrecv hello, from thread 1' 15: Received: 'Sendrecv hello, from thread 2' 15: Received: 'Sendrecv hello, from thread 0' 15: 15: Starting MPI_Bcast test 15: Received: 'Broadcast message 0 from 0' 15: Received: 'Broadcast message 0 from 1' 15: Received: 'Broadcast message 0 from 2' 15: Received: 'Broadcast message 1 from 0' 15: Received: 'Broadcast message 1 from 1' 15: Received: 'Broadcast message 1 from 2' 15: 15: Starting MPI_Gather test 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Finishing.. 15/104 Test #15: threadMPI-alloc_check ..................... Passed 0.15 sec test 16 Start 16: TestUtilsUnitTests 16: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests 16: Test timeout computed to be: 60 16: [==========] Running 81 tests from 8 test suites. 16: [----------] Global test environment set-up. 16: [----------] 10 tests from InteractiveTestHelperTest 16: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 16: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 16: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 16: [----------] 10 tests from InteractiveTestHelperTest (6 ms total) 16: 16: [----------] 10 tests from NameOfTestFromTupleTest 16: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 16: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 16: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 16: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 16: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 16: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 16: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 16: 16: [----------] 3 tests from RefDataFilenameMakerTest 16: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 16: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 16: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 16: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 16: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 16: 16: [----------] 6 tests from PosixMemstreamTest 16: [ RUN ] PosixMemstreamTest.ConstructsAndDestructs 16: [ OK ] PosixMemstreamTest.ConstructsAndDestructs (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilClosed 16: [ OK ] PosixMemstreamTest.HasAStreamUntilClosed (0 ms) 16: [ RUN ] PosixMemstreamTest.CanFetchString 16: [ OK ] PosixMemstreamTest.CanFetchString (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilStringIsFetched 16: [ OK ] PosixMemstreamTest.HasAStreamUntilStringIsFetched (0 ms) 16: [ RUN ] PosixMemstreamTest.CanWriteToStream 16: [ OK ] PosixMemstreamTest.CanWriteToStream (0 ms) 16: [ RUN ] PosixMemstreamTest.CanCheckBufferWithContents 16: [ OK ] PosixMemstreamTest.CanCheckBufferWithContents (0 ms) 16: [----------] 6 tests from PosixMemstreamTest (0 ms total) 16: 16: [----------] 37 tests from ReferenceDataTest 16: [ RUN ] ReferenceDataTest.HandlesSimpleData 16: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 16: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 16: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringBlockData 16: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesVectorData 16: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceData 16: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectData 16: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 16: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingData 16: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedData 16: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnys 16: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 16: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 16: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 16: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 16: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 16: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 16: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 16: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 16: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (4 ms) 16: [ RUN ] ReferenceDataTest.HandlesReadingValues 16: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 16: [----------] 37 tests from ReferenceDataTest (7 ms total) 16: 16: [----------] 7 tests from FloatingPointDifferenceTest 16: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 16: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 16: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 16: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 16: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 16: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 16: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 16: 16: [----------] 4 tests from FloatingPointToleranceTest 16: [ RUN ] FloatingPointToleranceTest.UlpTolerance 16: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 16: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 16: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 16: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 16: 16: [----------] 4 tests from XvgTests 16: [ RUN ] XvgTests.CreateFile 16: [ OK ] XvgTests.CreateFile (0 ms) 16: [ RUN ] XvgTests.CheckMissing 16: [ OK ] XvgTests.CheckMissing (0 ms) 16: [ RUN ] XvgTests.CheckExtra 16: [ OK ] XvgTests.CheckExtra (0 ms) 16: [ RUN ] XvgTests.ReadIncorrect 16: [ OK ] XvgTests.ReadIncorrect (0 ms) 16: [----------] 4 tests from XvgTests (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 81 tests from 8 test suites ran. (16 ms total) 16: [ PASSED ] 81 tests. 16/104 Test #16: TestUtilsUnitTests ........................ Passed 0.05 sec test 17 Start 17: TestUtilsMpiUnitTests 17: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/testutils/tests 17: Test timeout computed to be: 60 17: [==========] Running 3 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 1 test from MpiSelfTest 17: [ RUN ] MpiSelfTest.Runs 17: [ OK ] MpiSelfTest.Runs (17 ms) 17: [----------] 1 test from MpiSelfTest (17 ms total) 17: 17: [----------] 2 tests from MpiRefDataTest 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank (7 ms) 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName (3 ms) 17: [----------] 2 tests from MpiRefDataTest (11 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 3 tests from 2 test suites ran. (29 ms total) 17: [ PASSED ] 3 tests. 17/104 Test #17: TestUtilsMpiUnitTests ..................... Passed 0.05 sec test 18 Start 18: UtilityUnitTests 18: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 18: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests 18: Test timeout computed to be: 60 18: [==========] Running 495 tests from 68 test suites. 18: [----------] Global test environment set-up. 18: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/0.Comparison 18: [ OK ] AllocatorTest/0.Comparison (0 ms) 18: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.Move 18: [ OK ] AllocatorTest/0.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/0 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/1.Comparison 18: [ OK ] AllocatorTest/1.Comparison (0 ms) 18: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.Move 18: [ OK ] AllocatorTest/1.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/1 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/2.Comparison 18: [ OK ] AllocatorTest/2.Comparison (0 ms) 18: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.Move 18: [ OK ] AllocatorTest/2.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/2 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/3.Comparison 18: [ OK ] AllocatorTest/3.Comparison (0 ms) 18: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.Move 18: [ OK ] AllocatorTest/3.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/3 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/4.Comparison 18: [ OK ] AllocatorTest/4.Comparison (0 ms) 18: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.Move 18: [ OK ] AllocatorTest/4.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/4 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator,gmx::PageAlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/5.Comparison 18: [ OK ] AllocatorTest/5.Comparison (0 ms) 18: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.Move 18: [ OK ] AllocatorTest/5.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/5 (0 ms total) 18: 18: [----------] 1 test from AllocatorUntypedTest 18: [ RUN ] AllocatorUntypedTest.Comparison 18: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 18: [----------] 1 test from AllocatorUntypedTest (0 ms total) 18: 18: [----------] 4 tests from EmptyArrayRefTest 18: [ RUN ] EmptyArrayRefTest.IsEmpty 18: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 18: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 18: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 18: 18: [----------] 1 test from EmptyConstArrayRefTest 18: [ RUN ] EmptyConstArrayRefTest.IsEmpty 18: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 18: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 18: 18: [----------] 8 tests from BoolType 18: [ RUN ] BoolType.ImplicitConversion 18: [ OK ] BoolType.ImplicitConversion (0 ms) 18: [ RUN ] BoolType.FalseByDefault 18: [ OK ] BoolType.FalseByDefault (0 ms) 18: [ RUN ] BoolType.Assignment 18: [ OK ] BoolType.Assignment (0 ms) 18: [ RUN ] BoolType.Copy 18: [ OK ] BoolType.Copy (0 ms) 18: [ RUN ] BoolType.ArrayRefCanBeCreated 18: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 18: [ RUN ] BoolType.CanBeCastToBool 18: [ OK ] BoolType.CanBeCastToBool (0 ms) 18: [ RUN ] BoolType.HasSizeOfBool 18: [ OK ] BoolType.HasSizeOfBool (0 ms) 18: [ RUN ] BoolType.HasAlignmentOfBool 18: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 18: [----------] 8 tests from BoolType (0 ms total) 18: 18: [----------] 4 tests from ArrayRefFromBoolTypeVector 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.Works 18: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 18: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 18: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 18: 18: [----------] 7 tests from CStringUtilityTest 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 18: [ RUN ] CStringUtilityTest.strip_comment 18: [ OK ] CStringUtilityTest.strip_comment (0 ms) 18: [ RUN ] CStringUtilityTest.upstring 18: [ OK ] CStringUtilityTest.upstring (0 ms) 18: [ RUN ] CStringUtilityTest.ltrim 18: [ OK ] CStringUtilityTest.ltrim (0 ms) 18: [ RUN ] CStringUtilityTest.rtrim 18: [ OK ] CStringUtilityTest.rtrim (0 ms) 18: [ RUN ] CStringUtilityTest.trim 18: [ OK ] CStringUtilityTest.trim (0 ms) 18: [----------] 7 tests from CStringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from DefaultInitializationAllocator 18: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 18: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 18: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 18: 18: [----------] 4 tests from EnumerationHelpersTest 18: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 18: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 18: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 18: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 18: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 18: 18: [----------] 1 test from EnumClassSuitsEnumerationArray 18: [ RUN ] EnumClassSuitsEnumerationArray.Works 18: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 18: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 18: 18: [----------] 18 tests from FixedCapacityVectorTest 18: [ RUN ] FixedCapacityVectorTest.IsEmpty 18: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 18: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PushWorks 18: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PopWorks 18: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ResizeWorks 18: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ClearWorks 18: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 18: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.AtThrows 18: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 18: [ RUN ] FixedCapacityVectorTest.IteratorWorks 18: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 18: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 18: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 18: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 18: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.DataWorks 18: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 18: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 18: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 18: 18: [----------] 7 tests from TreeValueTransformTest 18: [ RUN ] TreeValueTransformTest.SimpleTransforms 18: [ OK ] TreeValueTransformTest.SimpleTransforms (9 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 18: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 18: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromString 18: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 18: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 18: [ RUN ] TreeValueTransformTest.ScopedTransformRules 18: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 18: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 18: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 18: [----------] 7 tests from TreeValueTransformTest (16 ms total) 18: 18: [----------] 1 test from TreeValueTransformErrorTest 18: [ RUN ] TreeValueTransformErrorTest.ConversionError 18: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 18: [----------] 1 test from TreeValueTransformErrorTest (1 ms total) 18: 18: [----------] 9 tests from ListOfLists 18: [ RUN ] ListOfLists.EmptyListOfListsWorks 18: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 18: [ RUN ] ListOfLists.AppendWorks 18: [ OK ] ListOfLists.AppendWorks (0 ms) 18: [ RUN ] ListOfLists.EmptyListWorks 18: [ OK ] ListOfLists.EmptyListWorks (0 ms) 18: [ RUN ] ListOfLists.AppendAccessWorks 18: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 18: [ RUN ] ListOfLists.ClearWorks 18: [ OK ] ListOfLists.ClearWorks (0 ms) 18: [ RUN ] ListOfLists.OutOfRangeAccessThrows 18: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 18: [ RUN ] ListOfLists.FrontAndBackWork 18: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 18: [ RUN ] ListOfLists.ExtractsAndRestores 18: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 18: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 18: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 18: [----------] 9 tests from ListOfLists (0 ms total) 18: 18: [----------] 7 tests from LoggerTest 18: [ RUN ] LoggerTest.EmptyLoggerWorks 18: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToStream 18: [ OK ] LoggerTest.LogsToStream (0 ms) 18: [ RUN ] LoggerTest.LogsToFile 18: [ OK ] LoggerTest.LogsToFile (0 ms) 18: [ RUN ] LoggerTest.LevelFilteringWorks 18: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleStreams 18: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleFiles 18: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 18: [ RUN ] LoggerTest.LogsToStreamAndFile 18: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 18: [----------] 7 tests from LoggerTest (3 ms total) 18: 18: [----------] 7 tests from MessageStringCollectorTest 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 18: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 18: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveAssign 18: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 18: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 18: 18: [----------] 12 tests from MpiComm 18: [ RUN ] MpiComm.SingleRankNoComm 18: [ OK ] MpiComm.SingleRankNoComm (0 ms) 18: [ RUN ] MpiComm.CommWorld 18: [ OK ] MpiComm.CommWorld (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: ./src/gromacs/utility/tests/mpicomm.cpp:160: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:168: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:181: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:194: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 18: [ RUN ] MpiComm.ConstructorThrowsOnNull 18: ./src/gromacs/utility/tests/mpicomm.cpp:206: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull (0 ms) 18: [ RUN ] MpiComm.CopyConstructorWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:220: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CopyConstructorWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:243: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:259: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:281: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:298: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 18: [----------] 12 tests from MpiComm (0 ms total) 18: 18: [----------] 1 test from PathTest 18: [ RUN ] PathTest.StripSourcePrefixWorks 18: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 18: [----------] 1 test from PathTest (0 ms total) 18: 18: [----------] 2 tests from PhysicalNodeCommunicatorTest 18: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 18: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 18: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 18: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 18: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 18: 18: [----------] 5 tests from Range 18: [ RUN ] Range.EmptyRangeWorks 18: [ OK ] Range.EmptyRangeWorks (0 ms) 18: [ RUN ] Range.NonEmptyRangeWorks 18: [ OK ] Range.NonEmptyRangeWorks (0 ms) 18: [ RUN ] Range.BeginEnd 18: [ OK ] Range.BeginEnd (0 ms) 18: [ RUN ] Range.IsInRangeWorks 18: [ OK ] Range.IsInRangeWorks (0 ms) 18: [ RUN ] Range.IteratorWorks 18: [ OK ] Range.IteratorWorks (0 ms) 18: [----------] 5 tests from Range (0 ms total) 18: 18: [----------] 3 tests from ScopeGuardTest 18: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 18: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 18: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 18: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 18: [----------] 3 tests from ScopeGuardTest (0 ms total) 18: 18: [----------] 7 tests from StringConvert 18: [ RUN ] StringConvert.NoResultFromEptyString 18: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 18: [ RUN ] StringConvert.ThreeFloatsSuccessfully 18: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 18: [ RUN ] StringConvert.OneIntSucessfully 18: [ OK ] StringConvert.OneIntSucessfully (0 ms) 18: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 18: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 18: [ RUN ] StringConvert.ThrowsWhenWrongSize 18: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 18: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 18: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 18: [----------] 7 tests from StringConvert (0 ms total) 18: 18: [----------] 7 tests from StringToEnumValueConverterTest 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 18: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 18: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 18: 18: [----------] 9 tests from StringUtilityTest 18: [ RUN ] StringUtilityTest.StartsWith 18: [ OK ] StringUtilityTest.StartsWith (0 ms) 18: [ RUN ] StringUtilityTest.EndsWith 18: [ OK ] StringUtilityTest.EndsWith (0 ms) 18: [ RUN ] StringUtilityTest.StripSuffixIfPresent 18: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 18: [ RUN ] StringUtilityTest.StripString 18: [ OK ] StringUtilityTest.StripString (0 ms) 18: [ RUN ] StringUtilityTest.SplitString 18: [ OK ] StringUtilityTest.SplitString (0 ms) 18: [ RUN ] StringUtilityTest.SplitDelimitedString 18: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 18: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 18: [----------] 9 tests from StringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from FormatStringTest 18: [ RUN ] FormatStringTest.HandlesBasicFormatting 18: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 18: [ RUN ] FormatStringTest.HandlesLongStrings 18: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 18: [----------] 2 tests from FormatStringTest (0 ms total) 18: 18: [----------] 1 test from StringFormatterTest 18: [ RUN ] StringFormatterTest.HandlesBasicFormatting 18: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 18: [----------] 1 test from StringFormatterTest (0 ms total) 18: 18: [----------] 1 test from formatAndJoinTest 18: [ RUN ] formatAndJoinTest.Works 18: [ OK ] formatAndJoinTest.Works (0 ms) 18: [----------] 1 test from formatAndJoinTest (0 ms total) 18: 18: [----------] 1 test from JoinStringsTest 18: [ RUN ] JoinStringsTest.Works 18: [ OK ] JoinStringsTest.Works (0 ms) 18: [----------] 1 test from JoinStringsTest (0 ms total) 18: 18: [----------] 6 tests from ReplaceAllTest 18: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 18: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesNoMatches 18: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 18: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 18: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 18: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 18: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 18: [----------] 6 tests from ReplaceAllTest (0 ms total) 18: 18: [----------] 10 tests from TextLineWrapperTest 18: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 18: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 18: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 18: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectly 18: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (3 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndent 18: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 18: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 18: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 18: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 18: [----------] 10 tests from TextLineWrapperTest (6 ms total) 18: 18: [----------] 1 test from PrettyPrintListAsRangeTest 18: [ RUN ] PrettyPrintListAsRangeTest.Works 18: [ OK ] PrettyPrintListAsRangeTest.Works (0 ms) 18: [----------] 1 test from PrettyPrintListAsRangeTest (0 ms total) 18: 18: [----------] 1 test from CompileTimeStringJoin 18: [ RUN ] CompileTimeStringJoin.Works 18: [ OK ] CompileTimeStringJoin.Works (0 ms) 18: [----------] 1 test from CompileTimeStringJoin (0 ms total) 18: 18: [----------] 3 tests from TemplateMPTest 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 18: [----------] 3 tests from TemplateMPTest (0 ms total) 18: 18: [----------] 8 tests from TextWriterTest 18: [ RUN ] TextWriterTest.WritesLines 18: [ OK ] TextWriterTest.WritesLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInParts 18: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 18: [ RUN ] TextWriterTest.WritesWrappedLines 18: [ OK ] TextWriterTest.WritesWrappedLines (2 ms) 18: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 18: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 18: [ RUN ] TextWriterTest.TracksNewlines 18: [ OK ] TextWriterTest.TracksNewlines (0 ms) 18: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 18: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 18: [ RUN ] TextWriterTest.WritesIndentedLines 18: [ OK ] TextWriterTest.WritesIndentedLines (0 ms) 18: [ RUN ] TextWriterTest.ScopedIndenterWritesIndentedLines 18: [ OK ] TextWriterTest.ScopedIndenterWritesIndentedLines (0 ms) 18: [----------] 8 tests from TextWriterTest (5 ms total) 18: 18: [----------] 4 tests from DumpingTextTest 18: [ RUN ] DumpingTextTest.LegacyIndentingWorks 18: [ OK ] DumpingTextTest.LegacyIndentingWorks (0 ms) 18: [ RUN ] DumpingTextTest.ReportsWhenNotAvailableIdentically 18: [ OK ] DumpingTextTest.ReportsWhenNotAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.QuietWhenAvailableIdentically 18: [ OK ] DumpingTextTest.QuietWhenAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.PrintsTitleAndSizeIdentically 18: [ OK ] DumpingTextTest.PrintsTitleAndSizeIdentically (0 ms) 18: [----------] 4 tests from DumpingTextTest (1 ms total) 18: 18: [----------] 1 test from TypeTraitsTest 18: [ RUN ] TypeTraitsTest.IsIntegralConstant 18: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 18: [----------] 1 test from TypeTraitsTest (0 ms total) 18: 18: [----------] 41 tests from RVecTest 18: [ RUN ] RVecTest.CanBeStoredInVector 18: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAsMutable_rvec 18: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Array 18: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 18: [ RUN ] RVecTest.ComparesEqual 18: [ OK ] RVecTest.ComparesEqual (0 ms) 18: [ RUN ] RVecTest.ComparesUnequal 18: [ OK ] RVecTest.ComparesUnequal (0 ms) 18: [ RUN ] RVecTest.CanAddRVecToRvec 18: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanAddAssignRVecToRvec 18: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractRVecFromRvec 18: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 18: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanDotProductRVecByRvec 18: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanCrossProductRVecByRvec 18: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVecInplace 18: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 18: [ RUN ] RVecTest.CanScaleRVec 18: [ OK ] RVecTest.CanScaleRVec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVec 18: [ OK ] RVecTest.CanDivideRVec (0 ms) 18: [ RUN ] RVecTest.CanDoUnitvFromRVec 18: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanSqLengthOfRVec 18: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanLengthOfRVec 18: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToRVec 18: [ OK ] RVecTest.CanCastToRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToDVec 18: [ OK ] RVecTest.CanCastToDVec (0 ms) 18: [ RUN ] RVecTest.CanLeftScalarMultiply 18: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanRightScalarMultiply 18: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanGetUnitvFromRVec 18: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanGetSqLengthOfRVec 18: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanGetLengthOfRVec 18: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoCrossProductOfRVec 18: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoDotProductOfRVec 18: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanScaleByVector 18: [ OK ] RVecTest.CanScaleByVector (0 ms) 18: [ RUN ] RVecTest.CanNegate 18: [ OK ] RVecTest.CanNegate (0 ms) 18: [ RUN ] RVecTest.asIVec 18: [ OK ] RVecTest.asIVec (0 ms) 18: [ RUN ] RVecTest.elementWiseMin 18: [ OK ] RVecTest.elementWiseMin (0 ms) 18: [ RUN ] RVecTest.elementWiseMax 18: [ OK ] RVecTest.elementWiseMax (0 ms) 18: [ RUN ] RVecTest.WorksAs_dvec_Reference 18: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_ivec_Reference 18: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Reference 18: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 18: [ RUN ] RVecTest.CopyConstructorWorks 18: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 18: [ RUN ] RVecTest.CopyAssignmentWorks 18: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.MoveConstructorWorks 18: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 18: [ RUN ] RVecTest.MoveAssignmentWorks 18: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.UsableInConstexpr 18: [ OK ] RVecTest.UsableInConstexpr (0 ms) 18: [----------] 41 tests from RVecTest (0 ms total) 18: 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 18: 18: [----------] 11 tests from WithInputPaths/PathSearchTest 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (1 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (3 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 18: [----------] 11 tests from WithInputPaths/PathSearchTest (9 ms total) 18: 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 18: 18: [----------] 24 tests from Works/DumpingVectorsTest 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 (0 ms) 18: [----------] 24 tests from Works/DumpingVectorsTest (23 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 495 tests from 68 test suites ran. (72 ms total) 18: [ PASSED ] 485 tests. 18: [ SKIPPED ] 10 tests, listed below: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull 18: [ SKIPPED ] MpiComm.CopyConstructorWorks 18: [ SKIPPED ] MpiComm.AssigmentWorks 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf 18: 18: YOU HAVE 1 DISABLED TEST 18: 18/104 Test #18: UtilityUnitTests .......................... Passed 0.12 sec test 19 Start 19: MpiCommTests 19: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mpicomm-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MpiCommTests.xml" 19: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests 19: Test timeout computed to be: 60 19: [==========] Running 12 tests from 1 test suite. 19: [----------] Global test environment set-up. 19: [----------] 12 tests from MpiComm 19: [ RUN ] MpiComm.SingleRankNoComm 19: [ OK ] MpiComm.SingleRankNoComm (8 ms) 19: [ RUN ] MpiComm.CommWorld 19: [ OK ] MpiComm.CommWorld (27 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (43 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (47 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (115 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (60 ms) 19: [ RUN ] MpiComm.ConstructorThrowsOnNull 19: [ OK ] MpiComm.ConstructorThrowsOnNull (7 ms) 19: [ RUN ] MpiComm.CopyConstructorWorks 19: [ OK ] MpiComm.CopyConstructorWorks (12 ms) 19: [ RUN ] MpiComm.AssigmentWorks 19: [ OK ] MpiComm.AssigmentWorks (10 ms) 19: [ RUN ] MpiComm.AssigmentWorksForSelf 19: [ OK ] MpiComm.AssigmentWorksForSelf (4 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorks 19: [ OK ] MpiComm.MoveAssigmentWorks (9 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 19: [ OK ] MpiComm.MoveAssigmentWorksForSelf (6 ms) 19: [----------] 12 tests from MpiComm (356 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 12 tests from 1 test suite ran. (360 ms total) 19: [ PASSED ] 12 tests. 19/104 Test #19: MpiCommTests .............................. Passed 0.39 sec test 20 Start 20: UtilityMpiUnitTests 20: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/utility/tests 20: Test timeout computed to be: 60 20: [==========] Running 7 tests from 2 test suites. 20: [----------] Global test environment set-up. 20: [----------] 5 tests from CoordinateExceptionHandlingTest 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue (3 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly (3 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow (0 ms) 20: [----------] 5 tests from CoordinateExceptionHandlingTest (12 ms total) 20: 20: [----------] 2 tests from PhysicalNodeCommunicatorTest 20: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 20: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (4 ms) 20: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 20: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (3 ms) 20: [----------] 2 tests from PhysicalNodeCommunicatorTest (7 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 7 tests from 2 test suites ran. (26 ms total) 20: [ PASSED ] 7 tests. 20/104 Test #20: UtilityMpiUnitTests ....................... Passed 0.05 sec test 21 Start 21: MdlibUnitTest 21: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests 21: Test timeout computed to be: 60 21: [==========] Running 1042 tests from 29 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from EffectiveAtomDensity 21: [ RUN ] EffectiveAtomDensity.VolumeIndependence 21: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 21: [ RUN ] EffectiveAtomDensity.WeightingWorks 21: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 21: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 21: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 21: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 21: 21: [----------] 2 tests from AtomNonbondedAndKineticProperties 21: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 21: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 21: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 21: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 21: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 21: 21: [----------] 1 test from VerletBufferConstraintTest 21: [ RUN ] VerletBufferConstraintTest.EqualMasses 21: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 21: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 21: 21: [----------] 1 test from VerletBufferSize 21: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 21: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 21: [----------] 1 test from VerletBufferSize (0 ms total) 21: 21: [----------] 6 tests from CalcvirTest 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (7 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 21: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 21: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 21: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 21: [----------] 6 tests from CalcvirTest (10 ms total) 21: 21: [----------] 2 tests from PrEbinTest 21: [ RUN ] PrEbinTest.HandlesAverages 21: [ OK ] PrEbinTest.HandlesAverages (1 ms) 21: [ RUN ] PrEbinTest.HandlesEmptyAverages 21: [ OK ] PrEbinTest.HandlesEmptyAverages (3 ms) 21: [----------] 2 tests from PrEbinTest (4 ms total) 21: 21: [----------] 3 tests from EnergyDriftTracker 21: [ RUN ] EnergyDriftTracker.emptyWorks 21: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.onePointWorks 21: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 21: [ RUN ] EnergyDriftTracker.manyPointsWorks 21: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 21: [----------] 3 tests from EnergyDriftTracker (0 ms total) 21: 21: [----------] 4 tests from ShakeTest 21: [ RUN ] ShakeTest.ConstrainsOneBond 21: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 21: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 21: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 21: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 21: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 21: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 21: [----------] 4 tests from ShakeTest (0 ms total) 21: 21: [----------] 1 test from NullSignalTest 21: [ RUN ] NullSignalTest.NullSignallerWorks 21: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 21: [----------] 1 test from NullSignalTest (0 ms total) 21: 21: [----------] 7 tests from SignalTest 21: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 21: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 21: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 21: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 21: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 21: [----------] 7 tests from SignalTest (0 ms total) 21: 21: [----------] 13 tests from UpdateGroupsTest 21: [ RUN ] UpdateGroupsTest.WithEthaneUA 21: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 21: [ RUN ] UpdateGroupsTest.WithMethane 21: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithEthane 21: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 21: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 21: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 21: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFourSite 21: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 21: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 21: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 21: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 21: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 21: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 21: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 21: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 21: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 21: [----------] 13 tests from UpdateGroupsTest (0 ms total) 21: 21: [----------] 1 test from UpdateGroupsCog 21: [ RUN ] UpdateGroupsCog.ComputesCogs 21: [ OK ] UpdateGroupsCog.ComputesCogs (2 ms) 21: [----------] 1 test from UpdateGroupsCog (6 ms total) 21: 21: [----------] 3 tests from VSiteTest 21: [ RUN ] VSiteTest.VSiteLowerConstructingWorks 21: [ OK ] VSiteTest.VSiteLowerConstructingWorks (0 ms) 21: [ RUN ] VSiteTest.VSiteHigherConstructingThrows 21: [ OK ] VSiteTest.VSiteHigherConstructingThrows (2 ms) 21: [ RUN ] VSiteTest.VSiteEqualConstructingThrows 21: [ OK ] VSiteTest.VSiteEqualConstructingThrows (0 ms) 21: [----------] 3 tests from VSiteTest (2 ms total) 21: 21: [----------] 2 tests from WholeMoleculeTransform 21: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 21: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 21: [ RUN ] WholeMoleculeTransform.HandlesReordering 21: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 21: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 21: 21: [----------] 28 tests from WithParameters/ConstraintsTest 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (1 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (1 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (6 ms) 21: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 21: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (10 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 21: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 21: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 21: [----------] 28 tests from WithParameters/ConstraintsTest (50 ms total) 21: 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/0 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/1 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/2 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/3 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/4 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/5 (0 ms) 21: [ RUN ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 21: [ OK ] WithParameters/ConstraintsReorderingTest.DifferentSystemsWork/6 (1 ms) 21: [----------] 7 tests from WithParameters/ConstraintsReorderingTest (1 ms total) 21: 21: [----------] 11 tests from WithParameters/EnergyOutputTest 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (8 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (6 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 21: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 21: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (4 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (6 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (2 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (5 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (1 ms) 21: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 21: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 21: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (5 ms) 21: [----------] 11 tests from WithParameters/EnergyOutputTest (51 ms total) 21: 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 21: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 21: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 21: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 21: 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 21: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 21: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 21: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 21: 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 21: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 21: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 21: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 21: 21: [----------] 17 tests from WithParameters/LangevinTest 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (1 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (3 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (3 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (7 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (3 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (1 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 21: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 21: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 21: [----------] 17 tests from WithParameters/LangevinTest (33 ms total) 21: 21: [----------] 16 tests from WithParameters/LeapFrogTest 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (4 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (4 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (2 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (5 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (2 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (7 ms) 21: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 21: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 21: [----------] 16 tests from WithParameters/LeapFrogTest (47 ms total) 21: 21: [----------] 140 tests from Cubic/ParrRahmTest 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (2 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (6 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (1 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (3 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (4 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (3 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (3 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (3 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (2 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (7 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (1 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (1 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (1 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 21: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 21: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Cubic/ParrRahmTest (138 ms total) 21: 21: [----------] 140 tests from Rectilinear/ParrRahmTest 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (4 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (6 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (5 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (4 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 21: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 21: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Rectilinear/ParrRahmTest (100 ms total) 21: 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (3 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (3 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (1 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (2 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (1 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (2 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (1 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (7 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 21: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (96 ms total) 21: 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (1 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (4 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (5 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (6 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (6 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 21: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 21: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (97 ms total) 21: 21: [----------] 140 tests from TruncOct/ParrRahmTest 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (1 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (2 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (4 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (3 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (6 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (4 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (5 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (5 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (4 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (4 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (6 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (6 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (4 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 21: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 21: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from TruncOct/ParrRahmTest (148 ms total) 21: 21: [----------] 140 tests from Other/ParrRahmTest 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (5 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (4 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (3 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (5 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (5 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (4 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (6 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (4 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (3 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (4 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (4 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (6 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 21: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 21: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 21: [----------] 140 tests from Other/ParrRahmTest (142 ms total) 21: 21: [----------] 13 tests from WithParameters/SettleTest 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (4 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 21: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 21: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (5 ms) 21: [----------] 13 tests from WithParameters/SettleTest (30 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1042 tests from 29 test suites ran. (965 ms total) 21: [ PASSED ] 1042 tests. 21/104 Test #21: MdlibUnitTest ............................. Passed 9.79 sec test 22 Start 22: AwhTest 22: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/AwhTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/awh/tests 22: Test timeout computed to be: 60 22: [==========] Running 27 tests from 10 test suites. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from SerializationTest 22: [ RUN ] SerializationTest.CanSerializeDimParams 22: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeBiasParams 22: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 22: [ RUN ] SerializationTest.CanSerializeAwhParams 22: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 22: [----------] 3 tests from SerializationTest (0 ms total) 22: 22: [----------] 1 test from BiasTest 22: [ RUN ] BiasTest.DetectsCovering 22: [ OK ] BiasTest.DetectsCovering (5 ms) 22: [----------] 1 test from BiasTest (6 ms total) 22: 22: [----------] 1 test from biasGridTest 22: [ RUN ] biasGridTest.neighborhood 22: [ OK ] biasGridTest.neighborhood (4 ms) 22: [----------] 1 test from biasGridTest (4 ms total) 22: 22: [----------] 2 tests from BiasSharingTest 22: [ RUN ] BiasSharingTest.SharingWorks 22: [ OK ] BiasSharingTest.SharingWorks (12 ms) 22: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 22: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (51 ms) 22: [----------] 2 tests from BiasSharingTest (63 ms total) 22: 22: [----------] 2 tests from BiasFepLambdaStateTest 22: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 22: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 22: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 22: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 22: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) 22: 22: [----------] 8 tests from WithParameters/BiasTest 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (5 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 22: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 22: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 22: [----------] 8 tests from WithParameters/BiasTest (15 ms total) 22: 22: [----------] 2 tests from WithParameters/BiasStateTest 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 22: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 22: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 22: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 22: 22: [----------] 1 test from WithParameters/UserInputTest 22: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 22: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 22: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 22: 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (8 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (4 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (8 ms) 22: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 22: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (8 ms) 22: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (38 ms total) 22: 22: [----------] 3 tests from WithParameters/FrictionMetricTest 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 22: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 22: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (20 ms) 22: [----------] 3 tests from WithParameters/FrictionMetricTest (27 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 27 tests from 10 test suites ran. (159 ms total) 22: [ PASSED ] 27 tests. 22/104 Test #22: AwhTest ................................... Passed 0.21 sec test 23 Start 23: DensityFittingAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 23: Test timeout computed to be: 60 23: [==========] Running 18 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from DensityFittingTest 23: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 23: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 23: [ RUN ] DensityFittingTest.SingleAtom 23: [ OK ] DensityFittingTest.SingleAtom (20 ms) 23: [----------] 2 tests from DensityFittingTest (21 ms total) 23: 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest 23: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 23: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 23: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 23: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 23: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 23: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 23: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 23: 23: [----------] 1 test from DensityFittingForceProviderState 23: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 23: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 23: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 23: 23: [----------] 8 tests from DensityFittingOptionsTest 23: [ RUN ] DensityFittingOptionsTest.DefaultParameters 23: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 23: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 23: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 23: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 23: [ RUN ] DensityFittingOptionsTest.KvtToInternal 23: [ OK ] DensityFittingOptionsTest.KvtToInternal (12 ms) 23: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 23: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 23: [----------] 8 tests from DensityFittingOptionsTest (12 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 18 tests from 4 test suites ran. (34 ms total) 23: [ PASSED ] 18 tests. 23/104 Test #23: DensityFittingAppliedForcesUnitTest ....... Passed 0.08 sec test 24 Start 24: QMMMAppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 24: Test timeout computed to be: 60 24: [==========] Running 28 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 2 tests from QMMMInputGeneratorTest 24: [ RUN ] QMMMInputGeneratorTest.CanConstruct 24: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 24: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 24: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (1 ms) 24: [----------] 2 tests from QMMMInputGeneratorTest (1 ms total) 24: 24: [----------] 6 tests from QMMMTopologyPreprocessorTest 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Setting the LD random seed to -39102859 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (8 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Setting the LD random seed to -365129 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (8 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading -0.41000 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -10798612 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (6 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 63.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 129.093 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: Setting the LD random seed to -285553923 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (24 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: 24: NOTE 2 [file unknown]: 24: You are using constraints on all bonds, whereas the forcefield has been 24: parametrized only with constraints involving hydrogen atoms. We suggest 24: using constraints = h-bonds instead, this will also improve performance. 24: 24: 24: NOTE 3 [file unknown]: 24: For energy conservation with LINCS, lincs_iter should be 2 or larger. 24: 24: 24: Number of degrees of freedom in T-Coupling group rest is 42.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: NVE simulation: will use the initial temperature of 193.640 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 5 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 24: 24: WARNING 1 [file unknown]: 24: Total charge of your embedded system differs from classical system! 24: Consider manually spreading 0.11440 charge over MM atoms near to the 24: embedded region 24: 24: 24: 24: WARNING 2 [file unknown]: 24: Your embedded subsystem has a lot of constrained bonds. They probably 24: have been generated automatically. That could produce artifacts in the 24: simulation. Consider constraints = none in the mdp file. 24: 24: 24: Setting the LD random seed to -285474820 24: 24: Generated 2145 of the 2145 non-bonded parameter combinations 24: 24: Generated 2145 of the 2145 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 24: 24: turning all bonds into constraints... 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 24: Analysing residue names: 24: There are: 3 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (21 ms) 24: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Number of degrees of freedom in T-Coupling group rest is 45.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.3-Debian_1 (double precision) 24: Setting the LD random seed to -38978065 24: 24: Generated 3 of the 6 non-bonded parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'VSTEST' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 24: 24: Cleaning up constraints and constant bonded interactions with virtual sites 24: Analysing residue names: 24: There are: 1 Other residues 24: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (6 ms) 24: [----------] 6 tests from QMMMTopologyPreprocessorTest (77 ms total) 24: 24: [----------] 9 tests from QMMMOptionsTest 24: [ RUN ] QMMMOptionsTest.DefaultParameters 24: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 24: [ RUN ] QMMMOptionsTest.OptionSetsActive 24: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 24: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 24: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 24: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 24: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 24: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 24: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 24: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 24: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 24: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 24: [----------] 9 tests from QMMMOptionsTest (3 ms total) 24: 24: [----------] 3 tests from QMMMForceProviderStateTest 24: [ RUN ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint 24: [ OK ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent 24: [ OK ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent (0 ms) 24: [ RUN ] QMMMForceProviderStateTest.MissingStateWhenNoData 24: [ OK ] QMMMForceProviderStateTest.MissingStateWhenNoData (0 ms) 24: [----------] 3 tests from QMMMForceProviderStateTest (0 ms total) 24: 24: [----------] 1 test from QMMMForceProviderTest 24: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 24: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 24: [----------] 1 test from QMMMForceProviderTest (0 ms total) 24: 24: [----------] 1 test from QMMMTest 24: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 24: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 24: [----------] 1 test from QMMMTest (0 ms total) 24: 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink (0 ms) 24: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink 24: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink (0 ms) 24: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest (2 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 28 tests from 7 test suites ran. (90 ms total) 24: [ PASSED ] 28 tests. 24/104 Test #24: QMMMAppliedForcesUnitTest ................. Passed 0.12 sec test 25 Start 25: ColvarsAppliedForcesUnitTest 25: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests 25: Test timeout computed to be: 60 25: [==========] Running 16 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 1 test from ColvarsTest 25: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 25: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 25: [----------] 1 test from ColvarsTest (0 ms total) 25: 25: [----------] 6 tests from ColvarsOptionsTest 25: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 25: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (1 ms) 25: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (2 ms) 25: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 25: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.OptionSetsActive 25: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 25: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to -40410373 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (21 ms) 25: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 25: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 25: [----------] 6 tests from ColvarsOptionsTest (31 ms total) 25: 25: [----------] 4 tests from ColvarsPreProcessorTest 25: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to -16941121 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (4 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to -1075843785 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (9 ms) 25: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to 1590672895 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (11 ms) 25: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to -285278212 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (12 ms) 25: [----------] 4 tests from ColvarsPreProcessorTest (38 ms total) 25: 25: [----------] 5 tests from ColvarsForceProviderTest 25: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 25: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 25: [ RUN ] ColvarsForceProviderTest.SimpleInputs 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to 2147351955 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 25: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to -71704593 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (14 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to -3162257 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForces4water (29 ms) 25: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 66.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: NVE simulation: will use the initial temperature of 300.368 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.3-Debian_1 (double precision) 25: Setting the LD random seed to -1141376285 25: 25: Generated 2211 of the 2211 non-bonded parameter combinations 25: 25: Generated 2211 of the 2211 1-4 parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 25: Analysing residue names: 25: There are: 2 Protein residues 25: Analysing Protein... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (45 ms) 25: [----------] 5 tests from ColvarsForceProviderTest (93 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 16 tests from 4 test suites ran. (164 ms total) 25: [ PASSED ] 16 tests. 25/104 Test #25: ColvarsAppliedForcesUnitTest .............. Passed 0.19 sec test 26 Start 26: PlumedAppliedForcesUnitTests 26: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests 26: Test timeout computed to be: 60 26: [==========] Running 8 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 8 tests from PlumedOptionsTest 26: [ RUN ] PlumedOptionsTest.defaultConstructor 26: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 26: [ RUN ] PlumedOptionsTest.setTimeStep 26: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 26: [ RUN ] PlumedOptionsTest.setStartingBehavior 26: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFile 26: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 26: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 26: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 26: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 26: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 26: [ RUN ] PlumedOptionsTest.setTopology 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 21.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: 26: NOTE 2 [file angles1.top, line 72]: 26: In moleculetype 'butane' 4 atoms are not bound by a potential or 26: constraint to any other atom in the same moleculetype. Although 26: technically this might not cause issues in a simulation, this often means 26: that the user forgot to add a bond/potential/constraint or put multiple 26: molecules in the same moleculetype definition by mistake. Run with -v to 26: get information for each atom. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 26: NVE simulation: will use the initial temperature of 238.919 K for 26: determining the Verlet buffer size 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.3-Debian_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.3-Debian_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 17493.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 26: NVE simulation: will use the initial temperature of 67.983 K for 26: determining the Verlet buffer size 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.3-Debian_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.3-Debian_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: There were 2 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.3-Debian_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.3-Debian_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Number of degrees of freedom in T-Coupling group rest is 9.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: NVE simulation with an initial temperature of zero: will use a Verlet 26: buffer of 10%. Check your energy drift! 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.3-Debian_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.3-Debian_1 (double precision) 26: 26: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: For a correct single-point energy evaluation with nsteps = 0, use 26: continuation = yes to avoid constraining the input coordinates. 26: 26: Generating 1-4 interactions: fudge = 0.5 26: Number of degrees of freedom in T-Coupling group rest is 18.00 26: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 26: 26: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: NVE simulation: will use the initial temperature of 135.187 K for 26: determining the Verlet buffer size 26: 26: 26: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 26: You are using a plain Coulomb cut-off, which might produce artifacts. 26: You might want to consider using PME electrostatics. 26: 26: 26: 26: There were 3 NOTEs 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.3-Debian_1 (double precision) 26: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.3-Debian_1 (double precision) 26: Setting the LD random seed to 1508747263 26: 26: Generated 10 of the 10 non-bonded parameter combinations 26: 26: Generated 10 of the 10 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Water residues 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -115417345 26: 26: Generated 3 of the 3 non-bonded parameter combinations 26: 26: Excluding 3 bonded neighbours molecule type 'butane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/angles1.gro' 26: Analysing residue names: 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -537018499 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Argon' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon5832.gro' 26: Analysing residue names: 26: There are: 5832 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -339738633 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonA' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonB' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonC' 26: 26: Excluding 1 bonded neighbours molecule type 'ArgonD' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 26: Analysing residue names: 26: There are: 4 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -134293026 26: 26: Generated 1 of the 1 non-bonded parameter combinations 26: 26: Excluding 1 bonded neighbours molecule type 'Dipole' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 26: Analysing residue names: 26: There are: 2 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: This run will generate roughly 0 Mb of data 26: Setting the LD random seed to -243409861 26: 26: Generated 331705 of the 331705 non-bonded parameter combinations 26: 26: Generated 331705 of the 331705 1-4 parameter combinations 26: 26: Excluding 2 bonded neighbours molecule type 'SOL' 26: 26: Excluding 3 bonded neighbours molecule type 'methane' 26: 26: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc_and_methane.gro' 26: Analysing residue names: 26: There are: 1 Water residues 26: There are: 1 Other residues 26: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 26: 26: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 26: 26: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 26: 26: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 26: 26: Note that mdrun will redetermine rlist based on the actual pair-list setup 26: 26: This run will generate roughly 0 Mb of data 26: [ OK ] PlumedOptionsTest.setTopology (632 ms) 26: [----------] 8 tests from PlumedOptionsTest (640 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 8 tests from 1 test suite ran. (640 ms total) 26: [ PASSED ] 8 tests. 26/104 Test #26: PlumedAppliedForcesUnitTests .............. Passed 0.68 sec test 27 Start 27: PlumedMDTests 27: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/PlumedMDTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/plumed/tests 27: Test timeout computed to be: 600 27: [==========] Running 2 tests from 1 test suite. 27: [----------] Global test environment set-up. 27: [----------] 2 tests from SimplePlumedMD/PlumedRun 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 27: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 27: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 27: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 27: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 2 tests from 1 test suite ran. (25 ms total) 27: [ PASSED ] 0 tests. 27: [ SKIPPED ] 2 tests, listed below: 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 27: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 27/104 Test #27: PlumedMDTests ............................. Passed 0.04 sec test 28 Start 28: NNPotAppliedForcesUnitTest 28: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 28: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests 28: Test timeout computed to be: 60 28: [==========] Running 17 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 1 test from NNPotTest 28: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 28: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 28: [----------] 1 test from NNPotTest (0 ms total) 28: 28: [----------] 5 tests from NNPotOptionsTest 28: [ RUN ] NNPotOptionsTest.DefaultParameters 28: [ OK ] NNPotOptionsTest.DefaultParameters (1 ms) 28: [ RUN ] NNPotOptionsTest.OptionSetsActive 28: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 28: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 28: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 28: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (5 ms) 28: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 28: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 28: [----------] 5 tests from NNPotOptionsTest (7 ms total) 28: 28: [----------] 1 test from NNPotForceProviderTest 28: [ RUN ] NNPotForceProviderTest.CanConstruct 28: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 28: [----------] 1 test from NNPotForceProviderTest (0 ms total) 28: 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Setting the LD random seed to -1075187211 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 (4 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Setting the LD random seed to -146841604 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 (7 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Setting the LD random seed to -455238681 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 (7 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 21.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Setting the LD random seed to -8474883 28: 28: Generated 10 of the 10 non-bonded parameter combinations 28: 28: Generated 10 of the 10 1-4 parameter combinations 28: 28: Excluding 2 bonded neighbours molecule type 'SOL' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 28: Analysing residue names: 28: There are: 4 Water residues 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 (3 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Setting the LD random seed to -335544345 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 (26 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: Number of degrees of freedom in T-Coupling group rest is 63.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 129.093 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: Setting the LD random seed to -76187681 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 (13 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: 28: WARNING 1 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -375463945 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 (21 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Generating 1-4 interactions: fudge = 0.5 28: 28: NOTE 2 [file unknown]: 28: You are using constraints on all bonds, whereas the forcefield has been 28: parametrized only with constraints involving hydrogen atoms. We suggest 28: using constraints = h-bonds instead, this will also improve performance. 28: 28: 28: NOTE 3 [file unknown]: 28: For energy conservation with LINCS, lincs_iter should be 2 or larger. 28: 28: 28: Number of degrees of freedom in T-Coupling group rest is 42.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: NVE simulation: will use the initial temperature of 193.640 K for 28: determining the Verlet buffer size 28: 28: 28: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 5 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.3-Debian_1 (double precision) 28: 28: WARNING 1 [file unknown]: 28: Total charge of your embedded system differs from classical system! 28: Consider manually spreading 0.11440 charge over MM atoms near to the 28: embedded region 28: 28: 28: 28: WARNING 2 [file unknown]: 28: Your embedded subsystem has a lot of constrained bonds. They probably 28: have been generated automatically. That could produce artifacts in the 28: simulation. Consider constraints = none in the mdp file. 28: 28: 28: Setting the LD random seed to -33595545 28: 28: Generated 2145 of the 2145 non-bonded parameter combinations 28: 28: Generated 2145 of the 2145 1-4 parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 28: 28: turning all bonds into constraints... 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 28: Analysing residue names: 28: There are: 3 Protein residues 28: Analysing Protein... 28: 28: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 28: 28: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 28: 28: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 28: 28: Note that mdrun will redetermine rlist based on the actual pair-list setup 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 (18 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Setting the LD random seed to -942997761 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 (7 ms) 28: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 28: 28: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: For a correct single-point energy evaluation with nsteps = 0, use 28: continuation = yes to avoid constraining the input coordinates. 28: 28: Number of degrees of freedom in T-Coupling group rest is 45.00 28: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 28: 28: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: NVE simulation with an initial temperature of zero: will use a Verlet 28: buffer of 10%. Check your energy drift! 28: 28: 28: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 28: You are using a plain Coulomb cut-off, which might produce artifacts. 28: You might want to consider using PME electrostatics. 28: 28: 28: 28: There were 3 NOTEs 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.3-Debian_1 (double precision) 28: Setting the LD random seed to 2046332030 28: 28: Generated 3 of the 6 non-bonded parameter combinations 28: 28: Excluding 3 bonded neighbours molecule type 'VSTEST' 28: 28: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 28: 28: Cleaning up constraints and constant bonded interactions with virtual sites 28: Analysing residue names: 28: There are: 1 Other residues 28: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 28: 28: This run will generate roughly 0 Mb of data 28: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 (8 ms) 28: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest (119 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 17 tests from 4 test suites ran. (127 ms total) 28: [ PASSED ] 17 tests. 28/104 Test #28: NNPotAppliedForcesUnitTest ................ Passed 0.18 sec test 29 Start 29: AppliedForcesUnitTest 29: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 29: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/applied_forces/tests 29: Test timeout computed to be: 60 29: [==========] Running 3 tests from 1 test suite. 29: [----------] Global test environment set-up. 29: [----------] 3 tests from ElectricFieldTest 29: [ RUN ] ElectricFieldTest.Static 29: [ OK ] ElectricFieldTest.Static (0 ms) 29: [ RUN ] ElectricFieldTest.Oscillating 29: [ OK ] ElectricFieldTest.Oscillating (0 ms) 29: [ RUN ] ElectricFieldTest.Pulsed 29: [ OK ] ElectricFieldTest.Pulsed (0 ms) 29: [----------] 3 tests from ElectricFieldTest (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 3 tests from 1 test suite ran. (0 ms total) 29: [ PASSED ] 3 tests. 29/104 Test #29: AppliedForcesUnitTest ..................... Passed 0.03 sec test 30 Start 30: ListedForcesTest 30: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 30: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/listed_forces/tests 30: Test timeout computed to be: 60 30: [==========] Running 132 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from Bond/ListedForcesTest 30: [ RUN ] Bond/ListedForcesTest.Ifunc/0 30: [ OK ] Bond/ListedForcesTest.Ifunc/0 (1 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/1 30: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/2 30: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/3 30: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/4 30: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/5 30: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/6 30: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/7 30: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/8 30: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/9 30: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/10 30: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/11 30: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/12 30: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/13 30: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/14 30: [ OK ] Bond/ListedForcesTest.Ifunc/14 (4 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/15 30: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/16 30: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/17 30: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/18 30: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/19 30: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/20 30: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/21 30: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/22 30: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Bond/ListedForcesTest.Ifunc/23 30: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 30: [----------] 24 tests from Bond/ListedForcesTest (15 ms total) 30: 30: [----------] 33 tests from Angle/ListedForcesTest 30: [ RUN ] Angle/ListedForcesTest.Ifunc/0 30: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/1 30: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/2 30: [ OK ] Angle/ListedForcesTest.Ifunc/2 (2 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/3 30: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/4 30: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/5 30: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/6 30: [ OK ] Angle/ListedForcesTest.Ifunc/6 (5 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/7 30: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/8 30: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/9 30: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/10 30: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/11 30: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/12 30: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/13 30: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/14 30: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/15 30: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/16 30: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/17 30: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/18 30: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/19 30: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/20 30: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/21 30: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/22 30: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/23 30: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/24 30: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/25 30: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/26 30: [ OK ] Angle/ListedForcesTest.Ifunc/26 (2 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/27 30: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/28 30: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/29 30: [ OK ] Angle/ListedForcesTest.Ifunc/29 (6 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/30 30: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/31 30: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 30: [ RUN ] Angle/ListedForcesTest.Ifunc/32 30: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 30: [----------] 33 tests from Angle/ListedForcesTest (45 ms total) 30: 30: [----------] 18 tests from Dihedral/ListedForcesTest 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (3 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (2 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (2 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 30: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Dihedral/ListedForcesTest (22 ms total) 30: 30: [----------] 12 tests from Polarize/ListedForcesTest 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 30: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 30: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 30: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 30: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (3 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 30: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 30: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 30: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 30: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 30: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 30: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 30: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 30: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 30: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from Polarize/ListedForcesTest (19 ms total) 30: 30: [----------] 18 tests from Restraints/ListedForcesTest 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 30: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 30: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 30: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 30: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 30: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 30: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 30: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 30: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 30: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 30: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 30: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (2 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 30: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 30: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 30: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (2 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 30: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 30: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 30: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 30: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 30: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 30: [----------] 18 tests from Restraints/ListedForcesTest (20 ms total) 30: 30: [----------] 3 tests from BondZeroLength/ListedForcesTest 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 30: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 30: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total) 30: 30: [----------] 3 tests from AngleZero/ListedForcesTest 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (1 ms) 30: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 30: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 30: [----------] 3 tests from AngleZero/ListedForcesTest (3 ms total) 30: 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (4 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 30: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 30: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 30: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (15 ms total) 30: 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (4 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 30: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 30: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 30: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (8 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 132 tests from 9 test suites ran. (154 ms total) 30: [ PASSED ] 132 tests. 30/104 Test #30: ListedForcesTest .......................... Passed 0.20 sec test 31 Start 31: NbnxmTests 31: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nbnxm-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests 31: Test timeout computed to be: 60 31: [==========] Running 532 tests from 5 test suites. 31: [----------] Global test environment set-up. 31: [----------] 19 tests from KernelSetupTest 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 31: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 31: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 31: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 31: [ RUN ] KernelSetupTest.getCoulombKernelTypeNone 31: [ OK ] KernelSetupTest.getCoulombKernelTypeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 31: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 31: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 31: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 31: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 31: [----------] 19 tests from KernelSetupTest (0 ms total) 31: 31: [----------] 2 tests from SimdEnergyAccumulatorTest 31: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 31: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 31: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 31: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 31: 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 31: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 31: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 31: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 31: 31: [----------] 504 tests from Combinations/NbnxmKernelTest 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (10 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (8 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (50 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (7 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (7 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (7 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 31: Analytical Ewald is not implemented for the plain-C kernel, skip this test 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 31: There are no combination rule versions of the plain-C kernel 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (7 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (5 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (6 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (4 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 31: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 31: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 31: [----------] 504 tests from Combinations/NbnxmKernelTest (788 ms total) 31: 31: [----------] 4 tests from WithParameters/PlainPairlistTest 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 (3 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:241: Skipped 31: Cannot test or generate data for 2xNN kernels without suitable SIMD support 31: 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 (0 ms) 31: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 31: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 (0 ms) 31: [----------] 4 tests from WithParameters/PlainPairlistTest (4 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 532 tests from 5 test suites ran. (799 ms total) 31: [ PASSED ] 189 tests. 31: [ SKIPPED ] 343 tests, listed below: 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 31: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 31/104 Test #31: NbnxmTests ................................ Passed 0.85 sec test 32 Start 32: NbnxmGpuTests 32: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests 32: Test timeout computed to be: 60 32: This test program does NOT link in any test case. Please make sure this is intended. 32: [==========] Running 0 tests from 0 test suites. 32: [==========] 0 tests from 0 test suites ran. (0 ms total) 32: [ PASSED ] 0 tests. 32/104 Test #32: NbnxmGpuTests ............................. Passed 0.03 sec test 33 Start 33: GmxlibTests 33: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests 33: Test timeout computed to be: 60 33: [==========] Running 78 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 72 tests from NBInteraction/NonbondedFepTest 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (2 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (3 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (3 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (2 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (5 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (1 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (6 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (5 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (4 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (3 ms) 33: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 33: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 33: [----------] 72 tests from NBInteraction/NonbondedFepTest (100 ms total) 33: 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (1 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 33: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 33: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 33: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (4 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 78 tests from 2 test suites ran. (104 ms total) 33: [ PASSED ] 78 tests. 33/104 Test #33: GmxlibTests ............................... Passed 0.14 sec test 34 Start 34: GmxlibGpuTests 34: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/nonbonded-fep-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GmxlibGpuTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/nbnxm/tests 34: Test timeout computed to be: 60 34: This test program does NOT link in any test case. Please make sure this is intended. 34: [==========] Running 0 tests from 0 test suites. 34: [==========] 0 tests from 0 test suites ran. (0 ms total) 34: [ PASSED ] 0 tests. 34/104 Test #34: GmxlibGpuTests ............................ Passed 0.03 sec test 35 Start 35: CommandLineUnitTests 35: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests 35: Test timeout computed to be: 60 35: [==========] Running 60 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from CommandLineHelpModuleTest 35: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 35: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms) 35: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 35: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 35: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 35: [ OK ] CommandLineHelpModuleTest.ExportsHelp (4 ms) 35: [----------] 3 tests from CommandLineHelpModuleTest (7 ms total) 35: 35: [----------] 7 tests from CommandLineHelpWriterTest 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 35: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 35: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 35: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 35: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (4 ms) 35: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 35: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 35: [----------] 7 tests from CommandLineHelpWriterTest (8 ms total) 35: 35: [----------] 6 tests from CommandLineModuleManagerTest 35: [ RUN ] CommandLineModuleManagerTest.RunsModule 35: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 35: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 35: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 35: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 35: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 35: 35: [----------] 13 tests from CommandLineParserTest 35: [ RUN ] CommandLineParserTest.HandlesSingleValues 35: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 35: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 35: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 35: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms) 35: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 35: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesString 35: [ OK ] CommandLineParserTest.HandlesString (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 35: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 35: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 35: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 35: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 35: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 35: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 35: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 35: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 35: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 35: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 35: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 35: [----------] 13 tests from CommandLineParserTest (1 ms total) 35: 35: [----------] 6 tests from CommandLineProgramContextTest 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (1 ms) 35: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 35: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 35: [----------] 6 tests from CommandLineProgramContextTest (3 ms total) 35: 35: [----------] 3 tests from OutputNamesTest 35: [ RUN ] OutputNamesTest.CanBeSuffixed 35: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 35: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 35: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 35: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 35: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 35: [----------] 3 tests from OutputNamesTest (0 ms total) 35: 35: [----------] 22 tests from ParseCommonArgsTest 35: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 35: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 35: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 35: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 35: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 35: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 35: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 35: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 35: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 35: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 35: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 35: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 35: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 35: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 35: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 35: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 35: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 35: Value is /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 35: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 35: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 35: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (2 ms) 35: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 35: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 35: [----------] 22 tests from ParseCommonArgsTest (8 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 60 tests from 7 test suites ran. (30 ms total) 35: [ PASSED ] 60 tests. 35/104 Test #35: CommandLineUnitTests ...................... Passed 0.07 sec test 36 Start 36: DomDecTests 36: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/DomDecTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests 36: Test timeout computed to be: 60 36: [==========] Running 9 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 7 tests from HashedMap 36: [ RUN ] HashedMap.InsertsFinds 36: [ OK ] HashedMap.InsertsFinds (0 ms) 36: [ RUN ] HashedMap.NegativeKeysWork 36: [ OK ] HashedMap.NegativeKeysWork (0 ms) 36: [ RUN ] HashedMap.InsertsErases 36: [ OK ] HashedMap.InsertsErases (0 ms) 36: [ RUN ] HashedMap.InsertsOrAssigns 36: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 36: [ RUN ] HashedMap.Clears 36: [ OK ] HashedMap.Clears (0 ms) 36: [ RUN ] HashedMap.LinkedEntries 36: [ OK ] HashedMap.LinkedEntries (0 ms) 36: [ RUN ] HashedMap.ResizesTable 36: [ OK ] HashedMap.ResizesTable (0 ms) 36: [----------] 7 tests from HashedMap (0 ms total) 36: 36: [----------] 2 tests from LocalAtomSetManager 36: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 36: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 36: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 36: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 36: [----------] 2 tests from LocalAtomSetManager (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 9 tests from 2 test suites ran. (0 ms total) 36: [ PASSED ] 9 tests. 36/104 Test #36: DomDecTests ............................... Passed 0.03 sec test 37 Start 37: DomDecMpiTests 37: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/domdec/tests 37: Test timeout computed to be: 60 37: [==========] Running 8 tests from 1 test suite. 37: [----------] Global test environment set-up. 37: [----------] 8 tests from Works/HaloExchangeTest 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/0 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/0 (14 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/1 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/1 (19 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/2 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/2 (16 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/3 37: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/3 (31 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 (8 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 (4 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 (2 ms) 37: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/3 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 37: With thread-MPI, GPU halo exchange is only supported on CUDA 37: Google Test trace: 37: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 37: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 (8 ms) 37: [----------] 8 tests from Works/HaloExchangeTest (107 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 8 tests from 1 test suite ran. (108 ms total) 37: [ PASSED ] 4 tests. 37: [ SKIPPED ] 4 tests, listed below: 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 37: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 37/104 Test #37: DomDecMpiTests ............................ Passed 0.15 sec test 38 Start 38: EwaldUnitTests 38: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/ewald/tests 38: Test timeout computed to be: 60 38: [==========] Running 407 tests from 9 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from SeparatePmeRanksPermittedTest 38: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 38: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 38: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 38: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 38: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 38: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 38: 38: [----------] 108 tests from Pme_SplineAndSpreadTest 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (7 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (17 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (5 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (6 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (7 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (6 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (6 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (3 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (5 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (4 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (8 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (5 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 38: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 38: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (6 ms) 38: [----------] 108 tests from Pme_SplineAndSpreadTest (236 ms total) 38: 38: [----------] 64 tests from Pme_SolveTest 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (6 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from Pme_SolveTest (30 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (4 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 38: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (21 ms total) 38: 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (3 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 38: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 38: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (17 ms total) 38: 38: [----------] 64 tests from PmeDiffEps_SolveTest 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 38: Test is being skipped because: 38: CPU PME solve does not implement XYZ grid ordering 38: 38: 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 38: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 38: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 38: [----------] 64 tests from PmeDiffEps_SolveTest (34 ms total) 38: 38: [----------] 72 tests from Pme_GatherTest 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (2 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (3 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (4 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (5 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (5 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (5 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (6 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (6 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (5 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (4 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (6 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 38: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 38: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 38: [----------] 72 tests from Pme_GatherTest (116 ms total) 38: 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 38: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 38: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 38: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 38: 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (8 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (5 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (7 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (6 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (6 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (5 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (7 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (6 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (6 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (5 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (5 ms) 38: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 38: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 38: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (105 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 407 tests from 9 test suites ran. (564 ms total) 38: [ PASSED ] 311 tests. 38: [ SKIPPED ] 96 tests, listed below: 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 38: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 38/104 Test #38: EwaldUnitTests ............................ Passed 0.62 sec test 39 Start 39: FFTUnitTests 39: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fft/tests 39: Test timeout computed to be: 1920 39: [==========] Running 15 tests from 4 test suites. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from ManyFFTTest 39: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (3 ms) 39: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 39: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (10 ms) 39: [----------] 2 tests from ManyFFTTest (13 ms total) 39: 39: [----------] 1 test from FFTTest 39: [ RUN ] FFTTest.Real2DLength18_15Test 39: [ OK ] FFTTest.Real2DLength18_15Test (1 ms) 39: [----------] 1 test from FFTTest (1 ms total) 39: 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (2 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (7 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (2 ms) 39: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 39: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (3 ms) 39: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (27 ms total) 39: 39: [----------] 2 tests from Works/ParameterizedFFTTest3D 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (4 ms) 39: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 39: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 39: [----------] 2 tests from Works/ParameterizedFFTTest3D (11 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 15 tests from 4 test suites ran. (54 ms total) 39: [ PASSED ] 15 tests. 39/104 Test #39: FFTUnitTests .............................. Passed 0.10 sec test 40 Start 40: FmmInterfaceUnitTests 40: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/fmm-interface-tests "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/FmmInterfaceUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fmm/tests 40: Test timeout computed to be: 60 40: [==========] Running 18 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 10 tests from FmmMdpOptionsTest 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive 40: [ OK ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive 40: [ OK ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues 40: [ OK ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder 40: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive 40: [ OK ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive (1 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive (0 ms) 40: [ RUN ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive 40: [ OK ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive (0 ms) 40: [----------] 10 tests from FmmMdpOptionsTest (7 ms total) 40: 40: [----------] 4 tests from FmmMdpValidatorTest 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings 40: 40: ERROR 1 [file unknown]: 40: ExaFMM expansion order must be greater than 0. 40: 40: 40: ERROR 1 [file unknown]: 40: ExaFMM direct range must be 2 when using GROMACS as a direct provider. 40: 40: 40: ERROR 1 [file unknown]: 40: Adaptive tree cannot be used for FMM when GROMACS is the direct provider. 40: Use a uniform tree instead. 40: 40: 40: ERROR 1 [file unknown]: 40: Maximum particles per cell for FMM must be set to a positive value when 40: using an adaptive tree. 40: 40: 40: ERROR 1 [file unknown]: 40: Tree depth for FMM is determined based on the domain decomposition grid 40: when using GROMACS as the direct provider and should not be set by the 40: user. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings 40: 40: ERROR 1 [file unknown]: 40: FMSolvr tree depth must be greater than or equal to 0. 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings 40: [ OK ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings (0 ms) 40: [ RUN ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm 40: 40: ERROR 1 [file unknown]: 40: FMM requires Coulomb interaction type to be FMM, but got PME 40: 40: [ OK ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm (0 ms) 40: [----------] 4 tests from FmmMdpValidatorTest (0 ms total) 40: 40: [----------] 1 test from FmmForceProviderTest 40: [ RUN ] FmmForceProviderTest.ThrowsWhenConstructingStub 40: [ OK ] FmmForceProviderTest.ThrowsWhenConstructingStub (0 ms) 40: [----------] 1 test from FmmForceProviderTest (0 ms total) 40: 40: [----------] 3 tests from FmmForceProviderBuilderTest 40: [ RUN ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady 40: [ OK ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup 40: [ OK ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup (0 ms) 40: [ RUN ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider 40: [ OK ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider (0 ms) 40: [----------] 3 tests from FmmForceProviderBuilderTest (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 18 tests from 4 test suites ran. (9 ms total) 40: [ PASSED ] 18 tests. 40/104 Test #40: FmmInterfaceUnitTests ..................... Passed 0.05 sec test 41 Start 41: GpuUtilsUnitTests 41: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests 41: Test timeout computed to be: 60 41: [==========] Running 67 tests from 22 test suites. 41: [----------] Global test environment set-up. 41: [----------] 2 tests from ClfftInitializer 41: [ RUN ] ClfftInitializer.SingleInitializationWorks 41: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 41: [ RUN ] ClfftInitializer.TwoInitializationsWork 41: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 41: [----------] 2 tests from ClfftInitializer (0 ms total) 41: 41: [----------] 1 test from DevicesAvailable 41: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 41: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 41: [----------] 1 test from DevicesAvailable (0 ms total) 41: 41: [----------] 1 test from DeviceStreamManagerTest 41: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 41: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 41: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 41: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 41: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 41: 41: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 41: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 41: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 41: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 41: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 41: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 41: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 41: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 41: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 41: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 41: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Swap 41: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/0.Comparison 41: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 41: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 41: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Swap 41: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/1.Comparison 41: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 41: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Swap 41: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/2.Comparison 41: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 41: 41: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 41: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 41: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 41: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 41: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Swap 41: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 41: [ RUN ] HostAllocatorTestNoMem/3.Comparison 41: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 41: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 41: 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 41: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 41: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 41: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 41: 41: [----------] 1 test from HostAllocatorUntypedTest 41: [ RUN ] HostAllocatorUntypedTest.Comparison 41: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 41: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/0.Move 41: [ OK ] AllocatorTest/0.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/0 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/1.Move 41: [ OK ] AllocatorTest/1.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/1 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator,gmx::HostAllocationPolicy> 41: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/2.Move 41: [ OK ] AllocatorTest/2.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/2 (0 ms total) 41: 41: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 41: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 41: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 41: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 41: [ RUN ] AllocatorTest/3.Move 41: [ OK ] AllocatorTest/3.Move (0 ms) 41: [----------] 4 tests from AllocatorTest/3 (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 67 tests from 22 test suites ran. (0 ms total) 41: [ PASSED ] 67 tests. 41/104 Test #41: GpuUtilsUnitTests ......................... Passed 0.05 sec test 42 Start 42: GpuUtilsMpiTests 42: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/gpu_utils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GpuUtilsMpiTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gpu_utils/tests 42: Test timeout computed to be: 60 42: [==========] Running 15 tests from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message (6 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message (5 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message (3 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message (1 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message (0 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message (5 ms) 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/0_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/1_values_in_message 42: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/12000_values_in_message 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message (4 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message (3 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message (3 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message (3 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message (4 ms) 42: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 42: Can only test GPU-aware MPI on a build with an MPI library 42: Can only test GPU-aware MPI in a build with GPU support 42: Can only test GPU-aware MPI on ranks with available GPUs 42: GPU-aware MPI is not supported on at least one device and/or rank 42: 42: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message (3 ms) 42: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest (53 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 15 tests from 1 test suite ran. (53 ms total) 42: [ PASSED ] 0 tests. 42: [ SKIPPED ] 15 tests, listed below: 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 42: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 42: 42: YOU HAVE 3 DISABLED TESTS 42: 42/104 Test #42: GpuUtilsMpiTests .......................... Passed 0.09 sec test 43 Start 43: HardwareUnitTests 43: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/hardware/tests 43: Test timeout computed to be: 60 43: [==========] Running 22 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 1 test from CpuInfoTest 43: [ RUN ] CpuInfoTest.SupportLevel 43: [ OK ] CpuInfoTest.SupportLevel (0 ms) 43: [----------] 1 test from CpuInfoTest (0 ms total) 43: 43: [----------] 4 tests from HardwareTopologyTest 43: [ RUN ] HardwareTopologyTest.Execute 43: [ OK ] HardwareTopologyTest.Execute (18 ms) 43: [ RUN ] HardwareTopologyTest.HwlocExecute 43: [ OK ] HardwareTopologyTest.HwlocExecute (11 ms) 43: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 43: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (17 ms) 43: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 43: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (12 ms) 43: [----------] 4 tests from HardwareTopologyTest (62 ms total) 43: 43: [----------] 1 test from DevicesManagerTest 43: [ RUN ] DevicesManagerTest.Serialization 43: [ OK ] DevicesManagerTest.Serialization (0 ms) 43: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 43: [----------] 1 test from DevicesManagerTest (0 ms total) 43: 43: [----------] 1 test from UuidStringTest 43: [ RUN ] UuidStringTest.Works 43: [ OK ] UuidStringTest.Works (0 ms) 43: [----------] 1 test from UuidStringTest (0 ms total) 43: 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (12 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (16 ms total) 43: 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (8 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (4 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 43: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 43: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 43: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (15 ms total) 43: 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (3 ms) 43: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 43: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (6 ms) 43: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (12 ms total) 43: 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (44 ms) 43: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (44 ms total) 43: 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 43: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (62 ms) 43: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (62 ms total) 43: 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 43: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 43: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (81 ms) 43: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (81 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 22 tests from 10 test suites ran. (295 ms total) 43: [ PASSED ] 22 tests. 43: 43: YOU HAVE 1 DISABLED TEST 43: 43/104 Test #43: HardwareUnitTests ......................... Passed 0.32 sec test 44 Start 44: MathUnitTests 44: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/math/tests 44: Test timeout computed to be: 60 44: [==========] Running 293 tests from 40 test suites. 44: [----------] Global test environment set-up. 44: [----------] 1 test from EmptyArrayRefWithPaddingTest 44: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 44: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 44: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 44: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 44: 44: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 44: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 44: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 44: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 44: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 44: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 44: 44: [----------] 2 tests from InvertBoxMatrixTest 44: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 44: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 44: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 44: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 44: 44: [----------] 8 tests from ComplexNumberTest 44: [ RUN ] ComplexNumberTest.RealComplexMultiply 44: [ OK ] ComplexNumberTest.RealComplexMultiply (3 ms) 44: [ RUN ] ComplexNumberTest.RealComplexExp 44: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAdd 44: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexSubtract 44: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexMultiply 44: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexDivision 44: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexConjugate 44: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 44: [ RUN ] ComplexNumberTest.ComplexAbs2 44: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 44: [----------] 8 tests from ComplexNumberTest (6 ms total) 44: 44: [----------] 11 tests from TranslateAndScaleTest 44: [ RUN ] TranslateAndScaleTest.identityTransformation 44: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 44: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 44: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 44: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingIdentity 44: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 44: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 44: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 44: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 44: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 44: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 44: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 44: 44: [----------] 3 tests from AffineTransformationTest 44: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 44: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 44: [ RUN ] AffineTransformationTest.applyTransformationToVectors 44: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 44: [ RUN ] AffineTransformationTest.retrieveGradient 44: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 44: [----------] 3 tests from AffineTransformationTest (0 ms total) 44: 44: [----------] 14 tests from DensitySimilarityTest 44: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 44: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 44: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 44: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 44: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 44: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 44: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (21 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (12 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 44: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 44: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationCorrect 44: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 44: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 44: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 44: [----------] 14 tests from DensitySimilarityTest (36 ms total) 44: 44: [----------] 6 tests from StructureSimilarityTest 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 44: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 44: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 44: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 44: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 44: [----------] 6 tests from StructureSimilarityTest (3 ms total) 44: 44: [----------] 8 tests from ExponentialMovingAverage 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 44: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 44: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 44: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 44: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 44: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 44: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 44: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 44: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 44: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 44: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 44: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 44: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 44: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 44: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 44: 44: [----------] 21 tests from FunctionTest 44: [ RUN ] FunctionTest.StaticLog2 44: [ OK ] FunctionTest.StaticLog2 (0 ms) 44: [ RUN ] FunctionTest.Log2I32Bit 44: [ OK ] FunctionTest.Log2I32Bit (0 ms) 44: [ RUN ] FunctionTest.Log2I64Bit 44: [ OK ] FunctionTest.Log2I64Bit (0 ms) 44: [ RUN ] FunctionTest.GreatestCommonDivisor 44: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 44: [ RUN ] FunctionTest.InvsqrtFloat 44: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvsqrtDouble 44: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvsqrtInteger 44: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 44: [ RUN ] FunctionTest.InvcbrtFloat 44: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 44: [ RUN ] FunctionTest.InvcbrtDouble 44: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 44: [ RUN ] FunctionTest.InvcbrtInteger 44: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 44: [ RUN ] FunctionTest.SixthrootFloat 44: [ OK ] FunctionTest.SixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.SixthrootDouble 44: [ OK ] FunctionTest.SixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.SixthrootInteger 44: [ OK ] FunctionTest.SixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootFloat 44: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootDouble 44: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 44: [ RUN ] FunctionTest.InvsixthrootInteger 44: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 44: [ RUN ] FunctionTest.Powers 44: [ OK ] FunctionTest.Powers (0 ms) 44: [ RUN ] FunctionTest.ErfInvFloat 44: [ OK ] FunctionTest.ErfInvFloat (1 ms) 44: [ RUN ] FunctionTest.ErfInvDouble 44: [ OK ] FunctionTest.ErfInvDouble (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 44: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 44: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 44: [----------] 21 tests from FunctionTest (14 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 44: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 44: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 44: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 44: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 44: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 44: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 44: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 44: 44: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 44: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 44: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 44: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 44: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 44: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 44: 44: [----------] 4 tests from GaussianOn1DLattice 44: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 44: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 44: [ RUN ] GaussianOn1DLattice.isCorrect 44: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 44: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 44: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 44: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 44: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 44: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 44: 44: [----------] 9 tests from GaussTransformTest 44: [ RUN ] GaussTransformTest.isZeroUponConstruction 44: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 44: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 44: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 44: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 44: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 44: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 44: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 44: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 44: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 44: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 44: [ RUN ] GaussTransformTest.view 44: [ OK ] GaussTransformTest.view (0 ms) 44: [----------] 9 tests from GaussTransformTest (0 ms total) 44: 44: [----------] 3 tests from DensityFittingForce 44: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 44: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 44: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 44: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 44: [ RUN ] DensityFittingForce.pullsTowardsDerivative 44: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 44: [----------] 3 tests from DensityFittingForce (0 ms total) 44: 44: [----------] 2 tests from InvertMatrixTest 44: [ RUN ] InvertMatrixTest.IdentityIsImpotent 44: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 44: [ RUN ] InvertMatrixTest.ComputesInverse 44: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 44: [----------] 2 tests from InvertMatrixTest (0 ms total) 44: 44: [----------] 28 tests from MatrixTest 44: [ RUN ] MatrixTest.canSetFromArray 44: [ OK ] MatrixTest.canSetFromArray (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallyFromList 44: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 44: [ RUN ] MatrixTest.canSetStaticallySingleValue 44: [ OK ] MatrixTest.canSetStaticallySingleValue (0 ms) 44: [ RUN ] MatrixTest.canConstructAndFill 44: [ OK ] MatrixTest.canConstructAndFill (0 ms) 44: [ RUN ] MatrixTest.canSetValues 44: [ OK ] MatrixTest.canSetValues (0 ms) 44: [ RUN ] MatrixTest.canCopyAssign 44: [ OK ] MatrixTest.canCopyAssign (0 ms) 44: [ RUN ] MatrixTest.canSwap 44: [ OK ] MatrixTest.canSwap (0 ms) 44: [ RUN ] MatrixTest.staticMultiDimArrayExtent 44: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MatrixTest.canAddMatrix 44: [ OK ] MatrixTest.canAddMatrix (0 ms) 44: [ RUN ] MatrixTest.canAddAssignMatrix 44: [ OK ] MatrixTest.canAddAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractMatrix 44: [ OK ] MatrixTest.canSubtractMatrix (0 ms) 44: [ RUN ] MatrixTest.canSubtractAssignMatrix 44: [ OK ] MatrixTest.canSubtractAssignMatrix (0 ms) 44: [ RUN ] MatrixTest.canNegateMatrix 44: [ OK ] MatrixTest.canNegateMatrix (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarMultiplication 44: [ OK ] MatrixTest.MatrixScalarMultiplication (0 ms) 44: [ RUN ] MatrixTest.MatrixScalarDivision 44: [ OK ] MatrixTest.MatrixScalarDivision (0 ms) 44: [ RUN ] MatrixTest.MatrixVectorMultiplicationOperator 44: [ OK ] MatrixTest.MatrixVectorMultiplicationOperator (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 44: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 44: [ RUN ] MatrixTest.MatrixMatrixMultiplication 44: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 44: [ RUN ] MatrixTest.determinantWorks 44: [ OK ] MatrixTest.determinantWorks (0 ms) 44: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 44: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 44: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 44: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 44: [ RUN ] MatrixTest.traceWorks 44: [ OK ] MatrixTest.traceWorks (0 ms) 44: [ RUN ] MatrixTest.transposeWorks 44: [ OK ] MatrixTest.transposeWorks (0 ms) 44: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 44: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 44: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 44: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.canFillLegacyMatrix 44: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 44: [ RUN ] MatrixTest.IdentityMatrix 44: [ OK ] MatrixTest.IdentityMatrix (0 ms) 44: [ RUN ] MatrixTest.DiagonalMatrix 44: [ OK ] MatrixTest.DiagonalMatrix (0 ms) 44: [----------] 28 tests from MatrixTest (0 ms total) 44: 44: [----------] 25 tests from MultiDimArrayTest 44: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 44: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 44: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 44: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 44: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 44: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 44: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 44: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 44: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 44: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 44: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 44: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 44: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapStatic 44: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 44: [ RUN ] MultiDimArrayTest.canSwapDynamic 44: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 44: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 44: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 44: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 44: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToView 44: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 44: [ RUN ] MultiDimArrayTest.conversionToConstView 44: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 44: [ RUN ] MultiDimArrayTest.viewBegin 44: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.viewEnd 44: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstBegin 44: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 44: [ RUN ] MultiDimArrayTest.constViewConstEnd 44: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 44: [----------] 25 tests from MultiDimArrayTest (0 ms total) 44: 44: [----------] 4 tests from MultiDimArrayToMdSpanTest 44: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 44: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 44: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 44: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 44: 44: [----------] 9 tests from NelderMeadSimplexTest 44: [ RUN ] NelderMeadSimplexTest.BestVertex 44: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.WorstVertex 44: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 44: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 44: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 44: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 44: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 44: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 44: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 44: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 44: [ RUN ] NelderMeadSimplexTest.OrientedLength 44: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 44: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 44: 44: [----------] 2 tests from NelderMead 44: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 44: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 44: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 44: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 44: [----------] 2 tests from NelderMead (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ResizeWorks 44: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorks 44: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanCopyAssign 44: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanMoveAssign 44: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/0.CanSwap 44: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ResizeWorks 44: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorks 44: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanCopyAssign 44: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanMoveAssign 44: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/1.CanSwap 44: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 44: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ResizeWorks 44: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorks 44: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanCopyAssign 44: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanMoveAssign 44: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/2.CanSwap 44: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ResizeWorks 44: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorks 44: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanCopyAssign 44: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanMoveAssign 44: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/3.CanSwap 44: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 44: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ResizeWorks 44: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorks 44: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanCopyAssign 44: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanMoveAssign 44: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/4.CanSwap 44: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ResizeWorks 44: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorks 44: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanCopyAssign 44: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanMoveAssign 44: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/5.CanSwap 44: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ResizeWorks 44: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorks 44: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanCopyAssign 44: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanMoveAssign 44: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/6.CanSwap 44: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 44: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ResizeWorks 44: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorks 44: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanCopyAssign 44: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanMoveAssign 44: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/7.CanSwap 44: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ResizeWorks 44: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorks 44: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanCopyAssign 44: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanMoveAssign 44: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/8.CanSwap 44: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 44: 44: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 44: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 44: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ResizeWorks 44: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorks 44: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 44: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 44: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 44: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 44: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 44: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanCopyAssign 44: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanMoveAssign 44: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 44: [ RUN ] PaddedVectorTest/9.CanSwap 44: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 44: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 293 tests from 40 test suites ran. (65 ms total) 44: [ PASSED ] 293 tests. 44/104 Test #44: MathUnitTests ............................. Passed 0.13 sec test 45 Start 45: MdrunUtilityUnitTests 45: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests 45: Test timeout computed to be: 60 45: [==========] Running 33 tests from 3 test suites. 45: [----------] Global test environment set-up. 45: [----------] 4 tests from MDModulesNotifierTest 45: [ RUN ] MDModulesNotifierTest.AddConsumer 45: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 45: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 45: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 45: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 45: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 45: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 45: 45: [----------] 1 test from PlainPairlistRanges 45: [ RUN ] PlainPairlistRanges.RmsdDistance 45: [ OK ] PlainPairlistRanges.RmsdDistance (0 ms) 45: [----------] 1 test from PlainPairlistRanges (0 ms total) 45: 45: [----------] 28 tests from ThreadAffinityTest 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 45: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 45: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 45: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 45: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 45: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 45: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms) 45: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 45: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 45: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 45: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 45: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndFullMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndFullMask (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask 45: [ OK ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask (0 ms) 45: [ RUN ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall 45: [ OK ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithSmt (41 ms) 45: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt 45: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem (0 ms) 45: [ RUN ] ThreadAffinityTest.PinsToECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToECoresInHybridSystem (7 ms) 45: [ RUN ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem 45: [ OK ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem (0 ms) 45: [----------] 28 tests from ThreadAffinityTest (56 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 33 tests from 3 test suites ran. (56 ms total) 45: [ PASSED ] 33 tests. 45/104 Test #45: MdrunUtilityUnitTests ..................... Passed 0.08 sec test 46 Start 46: MdrunUtilityMpiUnitTests 46: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdrunutility/tests 46: Test timeout computed to be: 60 46: [==========] Running 17 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 10 tests from ThreadAffinityMultiRankTest 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 46: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (133 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (110 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 46: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (102 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 46: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (95 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 46: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (80 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent (184 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame (192 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp (143 ms) 46: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken 46: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken (154 ms) 46: [----------] 10 tests from ThreadAffinityMultiRankTest (1204 ms total) 46: 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (107 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (115 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (132 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (40 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (71 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (19 ms) 46: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 46: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (69 ms) 46: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (557 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 17 tests from 2 test suites ran. (1767 ms total) 46: [ PASSED ] 17 tests. 46/104 Test #46: MdrunUtilityMpiUnitTests .................. Passed 1.79 sec test 47 Start 47: MDSpanTests 47: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdspan/tests 47: Test timeout computed to be: 60 47: [==========] Running 32 tests from 7 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from BasicAccessorPolicy 47: [ RUN ] BasicAccessorPolicy.Decay 47: [ OK ] BasicAccessorPolicy.Decay (0 ms) 47: [ RUN ] BasicAccessorPolicy.Access 47: [ OK ] BasicAccessorPolicy.Access (0 ms) 47: [ RUN ] BasicAccessorPolicy.Offset 47: [ OK ] BasicAccessorPolicy.Offset (0 ms) 47: [ RUN ] BasicAccessorPolicy.CopyAccessor 47: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 47: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 47: 47: [----------] 4 tests from ExtentsTest 47: [ RUN ] ExtentsTest.Construction 47: [ OK ] ExtentsTest.Construction (0 ms) 47: [ RUN ] ExtentsTest.PurelyStatic 47: [ OK ] ExtentsTest.PurelyStatic (0 ms) 47: [ RUN ] ExtentsTest.RankNought 47: [ OK ] ExtentsTest.RankNought (0 ms) 47: [ RUN ] ExtentsTest.Assignment 47: [ OK ] ExtentsTest.Assignment (0 ms) 47: [----------] 4 tests from ExtentsTest (0 ms total) 47: 47: [----------] 8 tests from MdSpanExtension 47: [ RUN ] MdSpanExtension.SlicingAllStatic 47: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingDynamic 47: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 47: [ RUN ] MdSpanExtension.SlicingAllStatic3D 47: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 47: [ RUN ] MdSpanExtension.SlicingEqualsView3D 47: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 47: [ RUN ] MdSpanExtension.additionWorks 47: [ OK ] MdSpanExtension.additionWorks (0 ms) 47: [ RUN ] MdSpanExtension.subtractionWorks 47: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 47: [ RUN ] MdSpanExtension.multiplicationWorks 47: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 47: [ RUN ] MdSpanExtension.divisionWorks 47: [ OK ] MdSpanExtension.divisionWorks (0 ms) 47: [----------] 8 tests from MdSpanExtension (0 ms total) 47: 47: [----------] 3 tests from LayoutTests 47: [ RUN ] LayoutTests.LayoutRightConstruction 47: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 47: [ RUN ] LayoutTests.LayoutRightProperties 47: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 47: [ RUN ] LayoutTests.LayoutRightOperator 47: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 47: [----------] 3 tests from LayoutTests (0 ms total) 47: 47: [----------] 1 test from MdSpanTest 47: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 47: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 47: [----------] 1 test from MdSpanTest (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/0.Rank 47: [ OK ] MdSpanTest/0.Rank (0 ms) 47: [ RUN ] MdSpanTest/0.DynamicRank 47: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/0.Extents 47: [ OK ] MdSpanTest/0.Extents (0 ms) 47: [ RUN ] MdSpanTest/0.Strides 47: [ OK ] MdSpanTest/0.Strides (0 ms) 47: [ RUN ] MdSpanTest/0.Properties 47: [ OK ] MdSpanTest/0.Properties (0 ms) 47: [ RUN ] MdSpanTest/0.Operator 47: [ OK ] MdSpanTest/0.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/0 (0 ms total) 47: 47: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 47: [ RUN ] MdSpanTest/1.Rank 47: [ OK ] MdSpanTest/1.Rank (0 ms) 47: [ RUN ] MdSpanTest/1.DynamicRank 47: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 47: [ RUN ] MdSpanTest/1.Extents 47: [ OK ] MdSpanTest/1.Extents (0 ms) 47: [ RUN ] MdSpanTest/1.Strides 47: [ OK ] MdSpanTest/1.Strides (0 ms) 47: [ RUN ] MdSpanTest/1.Properties 47: [ OK ] MdSpanTest/1.Properties (0 ms) 47: [ RUN ] MdSpanTest/1.Operator 47: [ OK ] MdSpanTest/1.Operator (0 ms) 47: [----------] 6 tests from MdSpanTest/1 (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 32 tests from 7 test suites ran. (0 ms total) 47: [ PASSED ] 32 tests. 47/104 Test #47: MDSpanTests ............................... Passed 0.03 sec test 48 Start 48: MdtypesUnitTest 48: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/mdtypes/tests 48: Test timeout computed to be: 60 48: [==========] Running 98 tests from 7 test suites. 48: [----------] Global test environment set-up. 48: [----------] 4 tests from ForeingLambdaTermsDhdl 48: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 48: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 48: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 48: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 48: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 48: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 48: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 48: 48: [----------] 4 tests from ObservablesReducerTest 48: [ RUN ] ObservablesReducerTest.CanMoveAssign 48: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 48: [ RUN ] ObservablesReducerTest.CanMoveConstruct 48: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 48: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 48: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 48: [----------] 4 tests from ObservablesReducerTest (0 ms total) 48: 48: [----------] 3 tests from CheckpointDataTest 48: [ RUN ] CheckpointDataTest.SingleDataTest 48: [ OK ] CheckpointDataTest.SingleDataTest (5 ms) 48: [ RUN ] CheckpointDataTest.MultiDataTest 48: [ OK ] CheckpointDataTest.MultiDataTest (29 ms) 48: [ RUN ] CheckpointDataTest.EmptyVectorTest 48: [ OK ] CheckpointDataTest.EmptyVectorTest (0 ms) 48: [----------] 3 tests from CheckpointDataTest (35 ms total) 48: 48: [----------] 7 tests from ForceBuffers 48: [ RUN ] ForceBuffers.ConstructsUnpinned 48: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsPinned 48: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 48: [ RUN ] ForceBuffers.ConstructsEmpty 48: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 48: [ RUN ] ForceBuffers.ResizeWorks 48: [ OK ] ForceBuffers.ResizeWorks (0 ms) 48: [ RUN ] ForceBuffers.PaddingWorks 48: [ OK ] ForceBuffers.PaddingWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyWorks 48: [ OK ] ForceBuffers.CopyWorks (0 ms) 48: [ RUN ] ForceBuffers.CopyDoesNotPin 48: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 48: [----------] 7 tests from ForceBuffers (0 ms total) 48: 48: [----------] 5 tests from MultipleTimeStepping 48: [ RUN ] MultipleTimeStepping.ChecksNumLevels 48: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 48: [ RUN ] MultipleTimeStepping.SelectsForceGroups 48: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksStepFactor 48: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 48: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 48: [ RUN ] MultipleTimeStepping.ChecksIntegrator 48: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 48: [----------] 5 tests from MultipleTimeStepping (0 ms total) 48: 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 48: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 48: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 48: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 48: 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 48: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 48: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 48: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 98 tests from 7 test suites ran. (36 ms total) 48: [ PASSED ] 98 tests. 48/104 Test #48: MdtypesUnitTest ........................... Passed 0.07 sec test 49 Start 49: OnlineHelpUnitTests 49: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/onlinehelp/tests 49: Test timeout computed to be: 60 49: [==========] Running 22 tests from 4 test suites. 49: [----------] Global test environment set-up. 49: [----------] 6 tests from TextTableFormatterTest 49: [ RUN ] TextTableFormatterTest.HandlesBasicCase 49: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesIndentation 49: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 49: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 49: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 49: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (4 ms) 49: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 49: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 49: [----------] 6 tests from TextTableFormatterTest (8 ms total) 49: 49: [----------] 3 tests from HelpManagerTest 49: [ RUN ] HelpManagerTest.HandlesRootTopic 49: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 49: [ RUN ] HelpManagerTest.HandlesSubTopics 49: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 49: [ RUN ] HelpManagerTest.HandlesInvalidTopics 49: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 49: [----------] 3 tests from HelpManagerTest (0 ms total) 49: 49: [----------] 2 tests from HelpTopicFormattingTest 49: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 49: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 49: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 49: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 49: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 49: 49: [----------] 11 tests from HelpWriterContextTest 49: [ RUN ] HelpWriterContextTest.FormatsParagraphs 49: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 49: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 49: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 49: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralText 49: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 49: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (4 ms) 49: [ RUN ] HelpWriterContextTest.FormatsBulletList 49: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 49: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 49: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsGridTable 49: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 49: [ RUN ] HelpWriterContextTest.FormatsTitles 49: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 49: [----------] 11 tests from HelpWriterContextTest (8 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 22 tests from 4 test suites ran. (18 ms total) 49: [ PASSED ] 22 tests. 49/104 Test #49: OnlineHelpUnitTests ....................... Passed 0.05 sec test 50 Start 50: OptionsUnitTests 50: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/options/tests 50: Test timeout computed to be: 60 50: [==========] Running 151 tests from 21 test suites. 50: [----------] Global test environment set-up. 50: [----------] 5 tests from AbstractOptionStorageTest 50: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 50: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 50: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 50: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 50: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 50: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 50: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 50: 50: [----------] 10 tests from FileNameOptionTest 50: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 50: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 50: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 50: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 50: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 50: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 50: [----------] 10 tests from FileNameOptionTest (0 ms total) 50: 50: [----------] 16 tests from FileNameOptionManagerTest 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 50: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 50: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 50: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 50: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 50: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 50: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 50: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 50: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 50: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 50: 50: [----------] 1 test from OptionsTest 50: [ RUN ] OptionsTest.FailsOnNonsafeStorage 50: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 50: [----------] 1 test from OptionsTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerTest 50: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 50: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 50: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 50: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMissingValue 50: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesExtraValue 50: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesGroups 50: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesSections 50: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 50: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 50: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 50: [----------] 9 tests from OptionsAssignerTest (0 ms total) 50: 50: [----------] 4 tests from OptionsAssignerBooleanTest 50: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 50: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 50: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 50: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 50: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 50: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 50: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerIntegerTest 50: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresToVector 50: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerInt64Test 50: [ RUN ] OptionsAssignerInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.StoresToVector 50: [ OK ] OptionsAssignerInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerInt64Test (0 ms total) 50: 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesOverflow 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesOverflow (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresToVector 50: [ OK ] OptionsAssignerUnsignedInt64Test.StoresToVector (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectors 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectors (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 50: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 50: [----------] 13 tests from OptionsAssignerUnsignedInt64Test (0 ms total) 50: 50: [----------] 5 tests from OptionsAssignerDoubleTest 50: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 50: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 50: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 50: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 50: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 50: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 50: 50: [----------] 9 tests from OptionsAssignerStringTest 50: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 50: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 50: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 50: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 50: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 50: 50: [----------] 6 tests from OptionsAssignerEnumTest 50: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 50: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 50: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 50: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 50: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 50: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 50: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 50: 50: [----------] 8 tests from RepeatingOptionSectionTest 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 50: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 50: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 50: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 50: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 50: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 50: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 50: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 50: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 50: 50: [----------] 1 test from TimeUnitManagerTest 50: [ RUN ] TimeUnitManagerTest.BasicOperations 50: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 50: [----------] 1 test from TimeUnitManagerTest (0 ms total) 50: 50: [----------] 4 tests from TimeUnitBehaviorTest 50: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 50: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 50: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 50: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 50: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 50: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 50: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 50: 50: [----------] 2 tests from TreeValueSupportAssignTest 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 50: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 50: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 50: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 50: 50: [----------] 1 test from TreeValueSupportAssignErrorTest 50: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 50: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 50: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 50: 50: [----------] 5 tests from TreeValueSupportCheckTest 50: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 50: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 50: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 50: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 50: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 50: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 50: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 50: 50: [----------] 6 tests from TreeValueSupportAdjustTest 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (5 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 50: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 50: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 50: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 50: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 50: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 50: [----------] 6 tests from TreeValueSupportAdjustTest (7 ms total) 50: 50: [----------] 7 tests from TreeValueSupportTest 50: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 50: [ OK ] TreeValueSupportTest.SupportsBooleanOption (4 ms) 50: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 50: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsInt64Option 50: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsStringOption 50: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsFloatOption 50: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 50: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 50: [ RUN ] TreeValueSupportTest.SupportsEnumOption 50: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 50: [----------] 7 tests from TreeValueSupportTest (7 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 151 tests from 21 test suites ran. (18 ms total) 50: [ PASSED ] 151 tests. 50/104 Test #50: OptionsUnitTests .......................... Passed 0.05 sec test 51 Start 51: PbcutilUnitTest 51: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 51: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pbcutil/tests 51: Test timeout computed to be: 60 51: [==========] Running 37 tests from 5 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ShiftTest 51: [ RUN ] ShiftTest.CoordinateShiftWorks 51: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 51: [----------] 1 test from ShiftTest (0 ms total) 51: 51: [----------] 2 tests from MShift 51: [ RUN ] MShift.shiftsAndUnshifts 51: [ OK ] MShift.shiftsAndUnshifts (0 ms) 51: [ RUN ] MShift.shiftsAndUnshiftsSelf 51: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 51: [----------] 2 tests from MShift (0 ms total) 51: 51: [----------] 5 tests from PbcTest 51: [ RUN ] PbcTest.CalcShiftsWorks 51: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 51: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 51: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 51: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 51: [----------] 5 tests from PbcTest (1 ms total) 51: 51: [----------] 2 tests from PbcEnumsTest 51: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 51: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 51: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 51: [----------] 2 tests from PbcEnumsTest (0 ms total) 51: 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (5 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (6 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (4 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 51: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 51: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 51: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (32 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 37 tests from 5 test suites ran. (33 ms total) 51: [ PASSED ] 37 tests. 51/104 Test #51: PbcutilUnitTest ........................... Passed 0.06 sec test 52 Start 52: RandomUnitTests 52: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/random/tests 52: Test timeout computed to be: 60 52: [==========] Running 44 tests from 10 test suites. 52: [----------] Global test environment set-up. 52: [----------] 4 tests from ExponentialDistributionTest 52: [ RUN ] ExponentialDistributionTest.Output 52: [ OK ] ExponentialDistributionTest.Output (4 ms) 52: [ RUN ] ExponentialDistributionTest.Logical 52: [ OK ] ExponentialDistributionTest.Logical (0 ms) 52: [ RUN ] ExponentialDistributionTest.Reset 52: [ OK ] ExponentialDistributionTest.Reset (0 ms) 52: [ RUN ] ExponentialDistributionTest.AltParam 52: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from ExponentialDistributionTest (4 ms total) 52: 52: [----------] 4 tests from GammaDistributionTest 52: [ RUN ] GammaDistributionTest.Output 52: [ OK ] GammaDistributionTest.Output (0 ms) 52: [ RUN ] GammaDistributionTest.Logical 52: [ OK ] GammaDistributionTest.Logical (0 ms) 52: [ RUN ] GammaDistributionTest.Reset 52: [ OK ] GammaDistributionTest.Reset (0 ms) 52: [ RUN ] GammaDistributionTest.AltParam 52: [ OK ] GammaDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from GammaDistributionTest (0 ms total) 52: 52: [----------] 4 tests from NormalDistributionTest 52: [ RUN ] NormalDistributionTest.Output 52: [ OK ] NormalDistributionTest.Output (0 ms) 52: [ RUN ] NormalDistributionTest.Logical 52: [ OK ] NormalDistributionTest.Logical (0 ms) 52: [ RUN ] NormalDistributionTest.Reset 52: [ OK ] NormalDistributionTest.Reset (0 ms) 52: [ RUN ] NormalDistributionTest.AltParam 52: [ OK ] NormalDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from NormalDistributionTest (0 ms total) 52: 52: [----------] 1 test from SeedTest 52: [ RUN ] SeedTest.makeRandomSeed 52: [ OK ] SeedTest.makeRandomSeed (0 ms) 52: [----------] 1 test from SeedTest (0 ms total) 52: 52: [----------] 6 tests from TabulatedNormalDistributionTest 52: [ RUN ] TabulatedNormalDistributionTest.Output14 52: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Output16 52: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 52: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Logical 52: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.Reset 52: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 52: [ RUN ] TabulatedNormalDistributionTest.AltParam 52: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 52: [----------] 6 tests from TabulatedNormalDistributionTest (6 ms total) 52: 52: [----------] 1 test from TabulatedNormalDistributionTableTest 52: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 52: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 52: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 52: 52: [----------] 6 tests from ThreeFry2x64Test 52: [ RUN ] ThreeFry2x64Test.Logical 52: [ OK ] ThreeFry2x64Test.Logical (0 ms) 52: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 52: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 52: [ RUN ] ThreeFry2x64Test.Reseed 52: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 52: [ RUN ] ThreeFry2x64Test.Discard 52: [ OK ] ThreeFry2x64Test.Discard (0 ms) 52: [ RUN ] ThreeFry2x64Test.InvalidCounter 52: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 52: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 52: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 52: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 52: 52: [----------] 4 tests from UniformIntDistributionTest 52: [ RUN ] UniformIntDistributionTest.Output 52: [ OK ] UniformIntDistributionTest.Output (6 ms) 52: [ RUN ] UniformIntDistributionTest.Logical 52: [ OK ] UniformIntDistributionTest.Logical (0 ms) 52: [ RUN ] UniformIntDistributionTest.Reset 52: [ OK ] UniformIntDistributionTest.Reset (0 ms) 52: [ RUN ] UniformIntDistributionTest.AltParam 52: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 52: [----------] 4 tests from UniformIntDistributionTest (6 ms total) 52: 52: [----------] 5 tests from UniformRealDistributionTest 52: [ RUN ] UniformRealDistributionTest.GenerateCanonical 52: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Output 52: [ OK ] UniformRealDistributionTest.Output (0 ms) 52: [ RUN ] UniformRealDistributionTest.Logical 52: [ OK ] UniformRealDistributionTest.Logical (0 ms) 52: [ RUN ] UniformRealDistributionTest.Reset 52: [ OK ] UniformRealDistributionTest.Reset (0 ms) 52: [ RUN ] UniformRealDistributionTest.AltParam 52: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 52: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 52: 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (6 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 52: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 52: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 52: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (10 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 44 tests from 10 test suites ran. (31 ms total) 52: [ PASSED ] 44 tests. 52/104 Test #52: RandomUnitTests ........................... Passed 0.06 sec test 53 Start 53: RestraintTests 53: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/RestraintTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/restraint/tests 53: Test timeout computed to be: 60 53: [==========] Running 1 test from 1 test suite. 53: [----------] Global test environment set-up. 53: [----------] 1 test from RestraintManager 53: [ RUN ] RestraintManager.restraintList 53: [ OK ] RestraintManager.restraintList (0 ms) 53: [----------] 1 test from RestraintManager (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 1 test from 1 test suite ran. (0 ms total) 53: [ PASSED ] 1 test. 53/104 Test #53: RestraintTests ............................ Passed 0.03 sec test 54 Start 54: SerializationUnitTests 54: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/serialization-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/SerializationUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/serialization/tests 54: Test timeout computed to be: 60 54: [==========] Running 9 tests from 2 test suites. 54: [----------] Global test environment set-up. 54: [----------] 5 tests from InMemorySerializerTest 54: [ RUN ] InMemorySerializerTest.Roundtrip 54: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 54: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 54: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 54: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 54: [ RUN ] InMemorySerializerTest.SizeIsCorrect 54: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 54: [----------] 5 tests from InMemorySerializerTest (0 ms total) 54: 54: [----------] 4 tests from KeyValueTreeSerializerTest 54: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 54: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 54: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 54: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 54: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 54: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 9 tests from 2 test suites ran. (2 ms total) 54: [ PASSED ] 9 tests. 54/104 Test #54: SerializationUnitTests .................... Passed 0.03 sec test 55 Start 55: TableUnitTests 55: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tables/tests 55: Test timeout computed to be: 60 55: [==========] Running 20 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 55: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/0.Sinc 55: [ OK ] SplineTableTest/0.Sinc (0 ms) 55: [ RUN ] SplineTableTest/0.LJ12 55: [ OK ] SplineTableTest/0.LJ12 (14 ms) 55: [ RUN ] SplineTableTest/0.PmeCorrection 55: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/0.TwoFunctions 55: [ OK ] SplineTableTest/0.TwoFunctions (23 ms) 55: [ RUN ] SplineTableTest/0.ThreeFunctions 55: [ OK ] SplineTableTest/0.ThreeFunctions (24 ms) 55: [ RUN ] SplineTableTest/0.Simd 55: [ OK ] SplineTableTest/0.Simd (6 ms) 55: [ RUN ] SplineTableTest/0.SimdTwoFunctions 55: [ OK ] SplineTableTest/0.SimdTwoFunctions (22 ms) 55: [----------] 10 tests from SplineTableTest/0 (94 ms total) 55: 55: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 55: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 55: [ RUN ] SplineTableTest/1.Sinc 55: [ OK ] SplineTableTest/1.Sinc (0 ms) 55: [ RUN ] SplineTableTest/1.LJ12 55: [ OK ] SplineTableTest/1.LJ12 (32 ms) 55: [ RUN ] SplineTableTest/1.PmeCorrection 55: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 55: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 55: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 55: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 55: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 55: [ RUN ] SplineTableTest/1.TwoFunctions 55: [ OK ] SplineTableTest/1.TwoFunctions (64 ms) 55: [ RUN ] SplineTableTest/1.ThreeFunctions 55: [ OK ] SplineTableTest/1.ThreeFunctions (66 ms) 55: [ RUN ] SplineTableTest/1.Simd 55: [ OK ] SplineTableTest/1.Simd (13 ms) 55: [ RUN ] SplineTableTest/1.SimdTwoFunctions 55: [ OK ] SplineTableTest/1.SimdTwoFunctions (49 ms) 55: [----------] 10 tests from SplineTableTest/1 (234 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 20 tests from 2 test suites ran. (329 ms total) 55: [ PASSED ] 20 tests. 55/104 Test #55: TableUnitTests ............................ Passed 0.36 sec test 56 Start 56: TaskAssignmentUnitTests 56: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/taskassignment/tests 56: Test timeout computed to be: 60 56: [==========] Running 3 tests from 2 test suites. 56: [----------] Global test environment set-up. 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 56: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 56: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 56: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 56: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 56: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 56: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 56: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 56: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 3 tests from 2 test suites ran. (0 ms total) 56: [ PASSED ] 3 tests. 56/104 Test #56: TaskAssignmentUnitTests ................... Passed 0.03 sec test 57 Start 57: GmxTimingTests 57: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/timing/tests 57: Test timeout computed to be: 60 57: [==========] Running 6 tests from 1 test suite. 57: [----------] Global test environment set-up. 57: [----------] 6 tests from TimingTest 57: [ RUN ] TimingTest.ElementCountingWorks 57: [ OK ] TimingTest.ElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.ElementNoCountingWorks 57: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementCountingWorks 57: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 57: [ RUN ] TimingTest.SubElementNoCountingWorks 57: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 57: [ RUN ] TimingTest.RunWallCycle 57: [ OK ] TimingTest.RunWallCycle (1 ms) 57: [ RUN ] TimingTest.RunWallCycleSub 57: [ OK ] TimingTest.RunWallCycleSub (0 ms) 57: [----------] 6 tests from TimingTest (1 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 6 tests from 1 test suite ran. (1 ms total) 57: [ PASSED ] 6 tests. 57/104 Test #57: GmxTimingTests ............................ Passed 0.03 sec test 58 Start 58: TopologyTest 58: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/TopologyTest.xml" 58: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/topology/tests 58: Test timeout computed to be: 60 58: [==========] Running 153 tests from 10 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from PdbAtomEntryTest 58: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 58: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 58: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 58: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 58: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 58: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 58: 58: [----------] 3 tests from ExclusionBlockTest 58: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 58: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 58: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 58: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 58: [ RUN ] ExclusionBlockTest.MergeExclusions 58: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 58: [----------] 3 tests from ExclusionBlockTest (0 ms total) 58: 58: [----------] 6 tests from InteractionListTest 58: [ RUN ] InteractionListTest.EmptyWorks 58: [ OK ] InteractionListTest.EmptyWorks (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArray 58: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 58: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 58: [ RUN ] InteractionListTest.CanAddInteractionPointer 58: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 58: [ RUN ] InteractionListTest.CanAddListToOtherList 58: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 58: [ RUN ] InteractionListTest.ClearingWorks 58: [ OK ] InteractionListTest.ClearingWorks (0 ms) 58: [----------] 6 tests from InteractionListTest (0 ms total) 58: 58: [----------] 3 tests from IndexTest 58: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.AnalyseWorksDefaultGroups (5 ms) 58: [ RUN ] IndexTest.WriteIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteIndexWorks (7 ms) 58: [ RUN ] IndexTest.WriteAndReadIndexWorks 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: The atomic radii are set according to: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: https://doi.org/10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] IndexTest.WriteAndReadIndexWorks (2 ms) 58: [----------] 3 tests from IndexTest (15 ms total) 58: 58: [----------] 4 tests from MtopTest 58: [ RUN ] MtopTest.RangeBasedLoop 58: [ OK ] MtopTest.RangeBasedLoop (0 ms) 58: [ RUN ] MtopTest.Operators 58: [ OK ] MtopTest.Operators (0 ms) 58: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 58: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 58: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 58: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 58: [----------] 4 tests from MtopTest (0 ms total) 58: 58: [----------] 2 tests from IListRangeTest 58: [ RUN ] IListRangeTest.RangeBasedLoopWorks 58: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 58: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 58: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 58: [----------] 2 tests from IListRangeTest (0 ms total) 58: 58: [----------] 13 tests from StringTableTest 58: [ RUN ] StringTableTest.AddSingleEntry 58: [ OK ] StringTableTest.AddSingleEntry (3 ms) 58: [ RUN ] StringTableTest.CanAccessWithAt 58: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 58: [ RUN ] StringTableTest.CanAccessWithBracket 58: [ OK ] StringTableTest.CanAccessWithBracket (7 ms) 58: [ RUN ] StringTableTest.ThrowsOutOfRange 58: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 58: [ RUN ] StringTableTest.StringCompareIsCorrect 58: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 58: [ RUN ] StringTableTest.AddTwoDistinctEntries 58: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] StringTableTest.TryToAddDuplicates 58: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 58: [ RUN ] StringTableTest.AddLargeNumberOfEntries 58: [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms) 58: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 58: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 58: [ RUN ] StringTableTest.CanWriteToBuffer 58: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 58: [ RUN ] StringTableTest.Roundtrip 58: [ OK ] StringTableTest.Roundtrip (0 ms) 58: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 58: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 58: [ RUN ] StringTableTest.CanCopyToLegacyTable 58: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 58: [----------] 13 tests from StringTableTest (19 ms total) 58: 58: [----------] 6 tests from LegacySymtabTest 58: [ RUN ] LegacySymtabTest.EmptyOnOpen 58: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 58: [ RUN ] LegacySymtabTest.AddSingleEntry 58: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 58: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 58: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 58: [ RUN ] LegacySymtabTest.TryToAddDuplicates 58: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 58: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 58: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 58: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 58: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 58: [----------] 6 tests from LegacySymtabTest (0 ms total) 58: 58: [----------] 5 tests from TopSortTest 58: [ RUN ] TopSortTest.WorksOnEmptyIdef 58: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 58: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 58: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 58: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 58: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 58: [----------] 5 tests from TopSortTest (0 ms total) 58: 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (6 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (2 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (3 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (2 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (6 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (5 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (3 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (5 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (3 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (6 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (3 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (6 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (5 ms) 58: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 58: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 58: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (138 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 153 tests from 10 test suites ran. (175 ms total) 58: [ PASSED ] 153 tests. 58: 58: YOU HAVE 1 DISABLED TEST 58: 58/104 Test #58: TopologyTest .............................. Passed 0.21 sec test 59 Start 59: PullTest 59: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/PullTest.xml" 59: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/pulling/tests 59: Test timeout computed to be: 60 59: [==========] Running 10 tests from 1 test suite. 59: [----------] Global test environment set-up. 59: [----------] 10 tests from PullTest 59: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 59: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 59: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 59: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 59: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 59: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 59: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 59: [ RUN ] PullTest.TransformationCoordSimple 59: [ OK ] PullTest.TransformationCoordSimple (0 ms) 59: [ RUN ] PullTest.TransformationCoordAdvanced 59: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 59: [ RUN ] PullTest.TransformationCoordTime 59: [ OK ] PullTest.TransformationCoordTime (0 ms) 59: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 59: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 59: [ RUN ] PullTest.TransformationCoordDummyExpression 59: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 59: [----------] 10 tests from PullTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 10 tests from 1 test suite ran. (2 ms total) 59: [ PASSED ] 10 tests. 59/104 Test #59: PullTest .................................. Passed 0.03 sec test 60 Start 60: SimdUnitTests 60: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/simd/tests 60: Test timeout computed to be: 60 60: [==========] Running 247 tests from 19 test suites. 60: [----------] Global test environment set-up. 60: [----------] 6 tests from SimdBootstrapTest 60: [ RUN ] SimdBootstrapTest.loadStore 60: [ OK ] SimdBootstrapTest.loadStore (0 ms) 60: [ RUN ] SimdBootstrapTest.loadU 60: [ OK ] SimdBootstrapTest.loadU (0 ms) 60: [ RUN ] SimdBootstrapTest.storeU 60: [ OK ] SimdBootstrapTest.storeU (0 ms) 60: [ RUN ] SimdBootstrapTest.loadStoreI 60: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 60: [ RUN ] SimdBootstrapTest.loadUI 60: [ OK ] SimdBootstrapTest.loadUI (0 ms) 60: [ RUN ] SimdBootstrapTest.storeUI 60: [ OK ] SimdBootstrapTest.storeUI (0 ms) 60: [----------] 6 tests from SimdBootstrapTest (0 ms total) 60: 60: [----------] 41 tests from SimdScalarTest 60: [ RUN ] SimdScalarTest.load 60: [ OK ] SimdScalarTest.load (0 ms) 60: [ RUN ] SimdScalarTest.loadU 60: [ OK ] SimdScalarTest.loadU (0 ms) 60: [ RUN ] SimdScalarTest.store 60: [ OK ] SimdScalarTest.store (0 ms) 60: [ RUN ] SimdScalarTest.storeU 60: [ OK ] SimdScalarTest.storeU (0 ms) 60: [ RUN ] SimdScalarTest.setZero 60: [ OK ] SimdScalarTest.setZero (0 ms) 60: [ RUN ] SimdScalarTest.andNot 60: [ OK ] SimdScalarTest.andNot (0 ms) 60: [ RUN ] SimdScalarTest.fma 60: [ OK ] SimdScalarTest.fma (0 ms) 60: [ RUN ] SimdScalarTest.fms 60: [ OK ] SimdScalarTest.fms (0 ms) 60: [ RUN ] SimdScalarTest.fnma 60: [ OK ] SimdScalarTest.fnma (0 ms) 60: [ RUN ] SimdScalarTest.fnms 60: [ OK ] SimdScalarTest.fnms (0 ms) 60: [ RUN ] SimdScalarTest.maskAdd 60: [ OK ] SimdScalarTest.maskAdd (0 ms) 60: [ RUN ] SimdScalarTest.maskzMul 60: [ OK ] SimdScalarTest.maskzMul (0 ms) 60: [ RUN ] SimdScalarTest.maskzFma 60: [ OK ] SimdScalarTest.maskzFma (0 ms) 60: [ RUN ] SimdScalarTest.abs 60: [ OK ] SimdScalarTest.abs (0 ms) 60: [ RUN ] SimdScalarTest.max 60: [ OK ] SimdScalarTest.max (0 ms) 60: [ RUN ] SimdScalarTest.min 60: [ OK ] SimdScalarTest.min (0 ms) 60: [ RUN ] SimdScalarTest.round 60: [ OK ] SimdScalarTest.round (0 ms) 60: [ RUN ] SimdScalarTest.trunc 60: [ OK ] SimdScalarTest.trunc (0 ms) 60: [ RUN ] SimdScalarTest.reduce 60: [ OK ] SimdScalarTest.reduce (0 ms) 60: [ RUN ] SimdScalarTest.testBits 60: [ OK ] SimdScalarTest.testBits (0 ms) 60: [ RUN ] SimdScalarTest.anyTrue 60: [ OK ] SimdScalarTest.anyTrue (0 ms) 60: [ RUN ] SimdScalarTest.selectByMask 60: [ OK ] SimdScalarTest.selectByMask (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMask 60: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 60: [ RUN ] SimdScalarTest.blend 60: [ OK ] SimdScalarTest.blend (0 ms) 60: [ RUN ] SimdScalarTest.cvtR2I 60: [ OK ] SimdScalarTest.cvtR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvttR2I 60: [ OK ] SimdScalarTest.cvttR2I (0 ms) 60: [ RUN ] SimdScalarTest.cvtI2R 60: [ OK ] SimdScalarTest.cvtI2R (0 ms) 60: [ RUN ] SimdScalarTest.cvtF2D 60: [ OK ] SimdScalarTest.cvtF2D (0 ms) 60: [ RUN ] SimdScalarTest.cvtD2D 60: [ OK ] SimdScalarTest.cvtD2D (0 ms) 60: [ RUN ] SimdScalarTest.loadI 60: [ OK ] SimdScalarTest.loadI (0 ms) 60: [ RUN ] SimdScalarTest.loadUI 60: [ OK ] SimdScalarTest.loadUI (0 ms) 60: [ RUN ] SimdScalarTest.storeI 60: [ OK ] SimdScalarTest.storeI (0 ms) 60: [ RUN ] SimdScalarTest.storeUI 60: [ OK ] SimdScalarTest.storeUI (0 ms) 60: [ RUN ] SimdScalarTest.andNotI 60: [ OK ] SimdScalarTest.andNotI (0 ms) 60: [ RUN ] SimdScalarTest.testBitsI 60: [ OK ] SimdScalarTest.testBitsI (0 ms) 60: [ RUN ] SimdScalarTest.selectByMaskI 60: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 60: [ RUN ] SimdScalarTest.selectByNotMaskI 60: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 60: [ RUN ] SimdScalarTest.blendI 60: [ OK ] SimdScalarTest.blendI (0 ms) 60: [ RUN ] SimdScalarTest.cvtB2IB 60: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 60: [ RUN ] SimdScalarTest.cvtIB2B 60: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 60: [ RUN ] SimdScalarTest.expandScalarsToTriplets 60: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 60: [----------] 41 tests from SimdScalarTest (0 ms total) 60: 60: [----------] 8 tests from SimdScalarUtilTest 60: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 60: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 60: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 60: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 60: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 60: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 60: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 60: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 60: 60: [----------] 37 tests from SimdScalarMathTest 60: [ RUN ] SimdScalarMathTest.copysign 60: [ OK ] SimdScalarMathTest.copysign (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPair 60: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 60: [ RUN ] SimdScalarMathTest.inv 60: [ OK ] SimdScalarMathTest.inv (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrt 60: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdScalarMathTest.log 60: [ OK ] SimdScalarMathTest.log (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2 60: [ OK ] SimdScalarMathTest.exp2 (0 ms) 60: [ RUN ] SimdScalarMathTest.exp 60: [ OK ] SimdScalarMathTest.exp (0 ms) 60: [ RUN ] SimdScalarMathTest.erf 60: [ OK ] SimdScalarMathTest.erf (0 ms) 60: [ RUN ] SimdScalarMathTest.erfc 60: [ OK ] SimdScalarMathTest.erfc (0 ms) 60: [ RUN ] SimdScalarMathTest.sincos 60: [ OK ] SimdScalarMathTest.sincos (0 ms) 60: [ RUN ] SimdScalarMathTest.sin 60: [ OK ] SimdScalarMathTest.sin (0 ms) 60: [ RUN ] SimdScalarMathTest.cos 60: [ OK ] SimdScalarMathTest.cos (0 ms) 60: [ RUN ] SimdScalarMathTest.tan 60: [ OK ] SimdScalarMathTest.tan (0 ms) 60: [ RUN ] SimdScalarMathTest.asin 60: [ OK ] SimdScalarMathTest.asin (0 ms) 60: [ RUN ] SimdScalarMathTest.acos 60: [ OK ] SimdScalarMathTest.acos (0 ms) 60: [ RUN ] SimdScalarMathTest.atan 60: [ OK ] SimdScalarMathTest.atan (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2 60: [ OK ] SimdScalarMathTest.atan2 (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrection 60: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 60: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.invSingleAccuracy 60: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 60: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.logSingleAccuracy 60: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 60: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.expSingleAccuracy 60: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 60: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 60: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 60: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 60: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 60: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 60: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 60: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 60: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 60: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 37 tests from SimdScalarMathTest (0 ms total) 60: 60: [----------] 1 test from SimdTest 60: [ RUN ] SimdTest.GmxAligned 60: [ OK ] SimdTest.GmxAligned (0 ms) 60: [----------] 1 test from SimdTest (0 ms total) 60: 60: [----------] 42 tests from SimdFloatingpointTest 60: [ RUN ] SimdFloatingpointTest.setZero 60: [ OK ] SimdFloatingpointTest.setZero (0 ms) 60: [ RUN ] SimdFloatingpointTest.set 60: [ OK ] SimdFloatingpointTest.set (0 ms) 60: [ RUN ] SimdFloatingpointTest.add 60: [ OK ] SimdFloatingpointTest.add (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskAdd 60: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 60: [ RUN ] SimdFloatingpointTest.sub 60: [ OK ] SimdFloatingpointTest.sub (0 ms) 60: [ RUN ] SimdFloatingpointTest.mul 60: [ OK ] SimdFloatingpointTest.mul (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzMul 60: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 60: [ RUN ] SimdFloatingpointTest.fma 60: [ OK ] SimdFloatingpointTest.fma (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzFma 60: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fms 60: [ OK ] SimdFloatingpointTest.fms (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnma 60: [ OK ] SimdFloatingpointTest.fnma (0 ms) 60: [ RUN ] SimdFloatingpointTest.fnms 60: [ OK ] SimdFloatingpointTest.fnms (0 ms) 60: [ RUN ] SimdFloatingpointTest.abs 60: [ OK ] SimdFloatingpointTest.abs (0 ms) 60: [ RUN ] SimdFloatingpointTest.neg 60: [ OK ] SimdFloatingpointTest.neg (0 ms) 60: [ RUN ] SimdFloatingpointTest.and 60: [ OK ] SimdFloatingpointTest.and (0 ms) 60: [ RUN ] SimdFloatingpointTest.or 60: [ OK ] SimdFloatingpointTest.or (0 ms) 60: [ RUN ] SimdFloatingpointTest.xor 60: [ OK ] SimdFloatingpointTest.xor (0 ms) 60: [ RUN ] SimdFloatingpointTest.andNot 60: [ OK ] SimdFloatingpointTest.andNot (0 ms) 60: [ RUN ] SimdFloatingpointTest.max 60: [ OK ] SimdFloatingpointTest.max (0 ms) 60: [ RUN ] SimdFloatingpointTest.min 60: [ OK ] SimdFloatingpointTest.min (0 ms) 60: [ RUN ] SimdFloatingpointTest.round 60: [ OK ] SimdFloatingpointTest.round (0 ms) 60: [ RUN ] SimdFloatingpointTest.roundMode 60: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 60: [ RUN ] SimdFloatingpointTest.trunc 60: [ OK ] SimdFloatingpointTest.trunc (0 ms) 60: [ RUN ] SimdFloatingpointTest.frexp 60: [ OK ] SimdFloatingpointTest.frexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.ldexp 60: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 60: [ RUN ] SimdFloatingpointTest.rsqrt 60: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRsqrt 60: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 60: [ RUN ] SimdFloatingpointTest.rcp 60: [ OK ] SimdFloatingpointTest.rcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.maskzRcp 60: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 60: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.selectByNotMask 60: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpNe 60: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLe 60: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 60: [ RUN ] SimdFloatingpointTest.cmpLt 60: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 60: [ RUN ] SimdFloatingpointTest.testBits 60: [ OK ] SimdFloatingpointTest.testBits (0 ms) 60: [ RUN ] SimdFloatingpointTest.andB 60: [ OK ] SimdFloatingpointTest.andB (0 ms) 60: [ RUN ] SimdFloatingpointTest.orB 60: [ OK ] SimdFloatingpointTest.orB (0 ms) 60: [ RUN ] SimdFloatingpointTest.anyTrueB 60: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 60: [ RUN ] SimdFloatingpointTest.blend 60: [ OK ] SimdFloatingpointTest.blend (0 ms) 60: [ RUN ] SimdFloatingpointTest.reduce 60: [ OK ] SimdFloatingpointTest.reduce (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 60: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 60: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 60: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 60: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 60: 60: [----------] 13 tests from SimdFloatingpointUtilTest 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 60: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 60: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 60: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 60: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 60: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 60: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 60: 60: [----------] 23 tests from SimdIntegerTest 60: [ RUN ] SimdIntegerTest.setZero 60: [ OK ] SimdIntegerTest.setZero (0 ms) 60: [ RUN ] SimdIntegerTest.set 60: [ OK ] SimdIntegerTest.set (0 ms) 60: [ RUN ] SimdIntegerTest.add 60: [ OK ] SimdIntegerTest.add (0 ms) 60: [ RUN ] SimdIntegerTest.sub 60: [ OK ] SimdIntegerTest.sub (0 ms) 60: [ RUN ] SimdIntegerTest.mul 60: [ OK ] SimdIntegerTest.mul (0 ms) 60: [ RUN ] SimdIntegerTest.and 60: [ OK ] SimdIntegerTest.and (0 ms) 60: [ RUN ] SimdIntegerTest.andNot 60: [ OK ] SimdIntegerTest.andNot (0 ms) 60: [ RUN ] SimdIntegerTest.or 60: [ OK ] SimdIntegerTest.or (0 ms) 60: [ RUN ] SimdIntegerTest.xor 60: [ OK ] SimdIntegerTest.xor (0 ms) 60: [ RUN ] SimdIntegerTest.extract 60: [ OK ] SimdIntegerTest.extract (0 ms) 60: [ RUN ] SimdIntegerTest.cvtR2I 60: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvttR2I 60: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 60: [ RUN ] SimdIntegerTest.cvtI2R 60: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 60: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 60: [ RUN ] SimdIntegerTest.cmpLt 60: [ OK ] SimdIntegerTest.cmpLt (0 ms) 60: [ RUN ] SimdIntegerTest.testBits 60: [ OK ] SimdIntegerTest.testBits (0 ms) 60: [ RUN ] SimdIntegerTest.andB 60: [ OK ] SimdIntegerTest.andB (0 ms) 60: [ RUN ] SimdIntegerTest.orB 60: [ OK ] SimdIntegerTest.orB (0 ms) 60: [ RUN ] SimdIntegerTest.anyTrue 60: [ OK ] SimdIntegerTest.anyTrue (0 ms) 60: [ RUN ] SimdIntegerTest.blend 60: [ OK ] SimdIntegerTest.blend (0 ms) 60: [ RUN ] SimdIntegerTest.cvtB2IB 60: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 60: [ RUN ] SimdIntegerTest.cvtIB2B 60: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 60: [----------] 23 tests from SimdIntegerTest (0 ms total) 60: 60: [----------] 56 tests from SimdMathTest 60: [ RUN ] SimdMathTest.generateTestPointsDouble 60: [ OK ] SimdMathTest.generateTestPointsDouble (5 ms) 60: [ RUN ] SimdMathTest.copysign 60: [ OK ] SimdMathTest.copysign (0 ms) 60: [ RUN ] SimdMathTest.invsqrt 60: [ OK ] SimdMathTest.invsqrt (0 ms) 60: [ RUN ] SimdMathTest.maskzInvsqrt 60: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPair 60: [ OK ] SimdMathTest.invsqrtPair (0 ms) 60: [ RUN ] SimdMathTest.sqrt 60: [ OK ] SimdMathTest.sqrt (0 ms) 60: [ RUN ] SimdMathTest.sqrtUnsafe 60: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 60: [ RUN ] SimdMathTest.inv 60: [ OK ] SimdMathTest.inv (0 ms) 60: [ RUN ] SimdMathTest.maskzInv 60: [ OK ] SimdMathTest.maskzInv (0 ms) 60: [ RUN ] SimdMathTest.cbrt 60: [ OK ] SimdMathTest.cbrt (0 ms) 60: [ RUN ] SimdMathTest.invcbrt 60: [ OK ] SimdMathTest.invcbrt (1 ms) 60: [ RUN ] SimdMathTest.log2 60: [ OK ] SimdMathTest.log2 (0 ms) 60: [ RUN ] SimdMathTest.log 60: [ OK ] SimdMathTest.log (0 ms) 60: [ RUN ] SimdMathTest.exp2 60: [ OK ] SimdMathTest.exp2 (0 ms) 60: [ RUN ] SimdMathTest.exp2Unsafe 60: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 60: [ RUN ] SimdMathTest.exp 60: [ OK ] SimdMathTest.exp (0 ms) 60: [ RUN ] SimdMathTest.expUnsafe 60: [ OK ] SimdMathTest.expUnsafe (0 ms) 60: [ RUN ] SimdMathTest.pow 60: [ OK ] SimdMathTest.pow (0 ms) 60: [ RUN ] SimdMathTest.powUnsafe 60: [ OK ] SimdMathTest.powUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erf 60: [ OK ] SimdMathTest.erf (0 ms) 60: [ RUN ] SimdMathTest.erfc 60: [ OK ] SimdMathTest.erfc (5 ms) 60: [ RUN ] SimdMathTest.sin 60: [ OK ] SimdMathTest.sin (0 ms) 60: [ RUN ] SimdMathTest.cos 60: [ OK ] SimdMathTest.cos (0 ms) 60: [ RUN ] SimdMathTest.tan 60: [ OK ] SimdMathTest.tan (0 ms) 60: [ RUN ] SimdMathTest.asin 60: [ OK ] SimdMathTest.asin (0 ms) 60: [ RUN ] SimdMathTest.acos 60: [ OK ] SimdMathTest.acos (0 ms) 60: [ RUN ] SimdMathTest.atan 60: [ OK ] SimdMathTest.atan (0 ms) 60: [ RUN ] SimdMathTest.atan2 60: [ OK ] SimdMathTest.atan2 (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrection 60: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrection 60: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 60: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 60: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracy 60: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.invSingleAccuracy 60: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.cbrtSingleAccuracy 60: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 60: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 60: [ RUN ] SimdMathTest.log2SingleAccuracy 60: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.logSingleAccuracy 60: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracy 60: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 60: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracy 60: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracy 60: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 60: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 60: [ RUN ] SimdMathTest.erfSingleAccuracy 60: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.erfcSingleAccuracy 60: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.sinSingleAccuracy 60: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.cosSingleAccuracy 60: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.tanSingleAccuracy 60: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.asinSingleAccuracy 60: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.acosSingleAccuracy 60: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atanSingleAccuracy 60: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.atan2SingleAccuracy 60: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 60: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 60: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 60: [----------] 56 tests from SimdMathTest (33 ms total) 60: 60: [----------] 1 test from EmptyArrayRefTest 60: [ RUN ] EmptyArrayRefTest.IsEmpty 60: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 60: [----------] 1 test from EmptyArrayRefTest (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/2 (1 ms total) 60: 60: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 60: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 60: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 60: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 60: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/0.Assignment 60: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefReadWriteTest/1.Assignment 60: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 60: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/0.Basic 60: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 60: 60: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 60: [ RUN ] ArrayRefArithmeticTest/1.Basic 60: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 60: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 60: 60: [----------] 3 tests from SimdVectorOperationsTest 60: [ RUN ] SimdVectorOperationsTest.iprod 60: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 60: [ RUN ] SimdVectorOperationsTest.norm2 60: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 60: [ RUN ] SimdVectorOperationsTest.cprod 60: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 60: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 247 tests from 19 test suites ran. (36 ms total) 60: [ PASSED ] 247 tests. 60/104 Test #60: SimdUnitTests ............................. Passed 0.07 sec test 61 Start 61: CompatibilityHelpersTests 61: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/compat/tests 61: Test timeout computed to be: 60 61: [==========] Running 9 tests from 6 test suites. 61: [----------] Global test environment set-up. 61: [----------] 4 tests from TemplateMPTest 61: [ RUN ] TemplateMPTest.MpWithIndexInt 61: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexIntBad 61: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexBool 61: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 61: [ RUN ] TemplateMPTest.MpWithIndexEnum 61: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 61: [----------] 4 tests from TemplateMPTest (0 ms total) 61: 61: [----------] 1 test from NotNullConstruction 61: [ RUN ] NotNullConstruction.Works 61: [ OK ] NotNullConstruction.Works (0 ms) 61: [----------] 1 test from NotNullConstruction (0 ms total) 61: 61: [----------] 1 test from NotNullCasting 61: [ RUN ] NotNullCasting.Works 61: [ OK ] NotNullCasting.Works (0 ms) 61: [----------] 1 test from NotNullCasting (0 ms total) 61: 61: [----------] 1 test from NotNullAssignment 61: [ RUN ] NotNullAssignment.Works 61: [ OK ] NotNullAssignment.Works (0 ms) 61: [----------] 1 test from NotNullAssignment (0 ms total) 61: 61: [----------] 1 test from MakeNotNull 61: [ RUN ] MakeNotNull.Works 61: [ OK ] MakeNotNull.Works (0 ms) 61: [----------] 1 test from MakeNotNull (0 ms total) 61: 61: [----------] 1 test from NotNull 61: [ RUN ] NotNull.WorksInContainers 61: [ OK ] NotNull.WorksInContainers (0 ms) 61: [----------] 1 test from NotNull (0 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 9 tests from 6 test suites ran. (0 ms total) 61: [ PASSED ] 9 tests. 61/104 Test #61: CompatibilityHelpersTests ................. Passed 0.02 sec test 62 Start 62: GmxAnaTest 62: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 62: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests 62: Test timeout computed to be: 600 62: [==========] Running 37 tests from 10 test suites. 62: [----------] Global test environment set-up. 62: [----------] 7 tests from Entropy 62: [ RUN ] Entropy.Schlitter_300_NoLinear 62: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 62: [ RUN ] Entropy.Schlitter_300_Linear 62: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (3 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 62: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 62: [ RUN ] Entropy.QuasiHarmonic_200_Linear 62: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 62: [ RUN ] Entropy.EntropyCompare_200_Linear 62: [ OK ] Entropy.EntropyCompare_200_Linear (1 ms) 62: [ RUN ] Entropy.EntropyCompare_300_Linear 62: [ OK ] Entropy.EntropyCompare_300_Linear (2 ms) 62: [----------] 7 tests from Entropy (14 ms total) 62: 62: [----------] 2 tests from GmxChiTest 62: [ RUN ] GmxChiTest.gmxchiWorksWithAll 62: Analyzing from residue 1 to residue 11 62: 10 residues with dihedrals found 62: 46 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 46 62: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithAll (894 ms) 62: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 62: Analyzing from residue 2 to residue 6 62: 5 residues with dihedrals found 62: 23 dihedrals found 62: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 62: j after resetting (nr. active dihedrals) = 23 62: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 62: Now calculating transitions... 62: Total number of transitions: 0 62: Now printing out transitions and OPs... 62: Now printing out rotamer occupancies... 62: Now calculating Chi product trajectories... 62: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 62: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (469 ms) 62: [----------] 2 tests from GmxChiTest (1505 ms total) 62: 62: [----------] 10 tests from MindistTest 62: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistWorksWithSingleAtoms (11 ms) 62: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (5 ms) 62: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms) 62: [ RUN ] MindistTest.mindistPicksUpContacts 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 62: [ RUN ] MindistTest.ngWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.ngWorks (1 ms) 62: [ RUN ] MindistTest.groupWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.groupWorks (2 ms) 62: [ RUN ] MindistTest.maxDistWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 2: 'atom3' 62: Selected 3: 'atoms12' 62: [ OK ] MindistTest.maxDistWorks (2 ms) 62: [ RUN ] MindistTest.noPbcWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 0: 'atom1' 62: Selected 1: 'atom2' 62: [ OK ] MindistTest.noPbcWorks (1 ms) 62: [ RUN ] MindistTest.resPerTimeWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 3: 'atoms12' 62: Selected 2: 'atom3' 62: [ OK ] MindistTest.resPerTimeWorks (1 ms) 62: [ RUN ] MindistTest.matrixWorks 62: Group 0 ( atom1) has 1 elements 62: Group 1 ( atom2) has 1 elements 62: Group 2 ( atom3) has 1 elements 62: Group 3 ( atoms12) has 2 elements 62: Group 4 ( atoms23) has 2 elements 62: Group 5 ( atoms123) has 3 elements 62: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Selected 5: 'atoms123' 62: Special case: making distance matrix between all atoms in group atoms123 62: [ OK ] MindistTest.matrixWorks (2 ms) 62: [----------] 10 tests from MindistTest (37 ms total) 62: 62: [----------] 1 test from GmxRmsTest 62: [ RUN ] GmxRmsTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Select group for least squares fit 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Select group for RMSD calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to 2146397695 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 1: 'Protein' 62: Selected 1: 'Protein' 62: [ OK ] GmxRmsTest.BasicOutputWorks (453 ms) 62: [----------] 1 test from GmxRmsTest (453 ms total) 62: 62: [----------] 1 test from GmxRmsdistTest 62: [ RUN ] GmxRmsdistTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: 62: rmsmax = 0.382568, rmscmax = 0.659498 62: Setting the LD random seed to -270057481 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 0: 'System' 62: [ OK ] GmxRmsdistTest.BasicOutputWorks (467 ms) 62: [----------] 1 test from GmxRmsdistTest (467 ms total) 62: 62: [----------] 1 test from GmxRmsfTest 62: [ RUN ] GmxRmsfTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Select group(s) for root mean square calculation 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 62: Setting the LD random seed to -1610629286 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 3: 'C-alpha' 62: [ OK ] GmxRmsfTest.BasicOutputWorks (360 ms) 62: [----------] 1 test from GmxRmsfTest (360 ms total) 62: 62: [----------] 1 test from GmxSorientTest 62: [ RUN ] GmxSorientTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Group 0 ( System) has 923 elements 62: Group 1 ( Protein) has 29 elements 62: Group 2 ( Protein-H) has 17 elements 62: Group 3 ( C-alpha) has 2 elements 62: Group 4 ( Backbone) has 6 elements 62: Group 5 ( MainChain) has 9 elements 62: Group 6 ( MainChain+Cb) has 11 elements 62: Group 7 ( MainChain+H) has 13 elements 62: Group 8 ( SideChain) has 16 elements 62: Group 9 ( SideChain-H) has 8 elements 62: Group 10 ( Prot-Masses) has 23 elements 62: Group 11 ( non-Protein) has 894 elements 62: Group 12 ( Water) has 894 elements 62: Group 13 ( SOL) has 894 elements 62: Group 14 ( non-Water) has 29 elements 62: Select a group: Select a group: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Average nr of molecules between 0 and 0.5 nm: 13.0 62: Average cos(theta1) between 0 and 0.5 nm: 0.103 62: Average 3cos2(theta2)-1 between 0 and 0.5 nm: -0.098 62: Setting the LD random seed to -562184225 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.pdb', all velocities are zero 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: Analysing residue names: 62: There are: 2 Protein residues 62: There are: 298 Water residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Select a group of reference particles and a solvent group: 62: Selected 1: 'Protein' 62: Selected 12: 'Water' 62: [ OK ] GmxSorientTest.BasicOutputWorks (37 ms) 62: [----------] 1 test from GmxSorientTest (39 ms total) 62: 62: [----------] 1 test from GmxRotmatTest 62: [ RUN ] GmxRotmatTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Setting the LD random seed to -21461894 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Selected 4: 'Backbone' 62: [ OK ] GmxRotmatTest.BasicOutputWorks (341 ms) 62: [----------] 1 test from GmxRotmatTest (341 ms total) 62: 62: [----------] 1 test from GmxSaltbrTest 62: [ RUN ] GmxSaltbrTest.BasicOutputWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.tpr, VERSION 2026.3-Debian_1 (double precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Setting the LD random seed to -3751979 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: This run will generate roughly 0 Mb of data 62: CG: SOL1-1 Q: -0.834 Atoms: 0 62: CG: SOL1-2 Q: 0.417 Atoms: 1 62: CG: SOL1-3 Q: 0.417 Atoms: 2 62: CG: SOL2-4 Q: -0.834 Atoms: 3 62: CG: SOL2-5 Q: 0.417 Atoms: 4 62: CG: SOL2-6 Q: 0.417 Atoms: 5 62: [ OK ] GmxSaltbrTest.BasicOutputWorks (13 ms) 62: [----------] 1 test from GmxSaltbrTest (13 ms total) 62: 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (2 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (8 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (2 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (9 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (2 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (2 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (4 ms) 62: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Group 0 ( System) has 6 elements 62: Group 1 ( Water) has 6 elements 62: Group 2 ( SOL) has 6 elements 62: Select a group: Reading frame 0 time 0.000 62: WARNING: If there are molecules in the input trajectory file 62: that are broken across periodic boundaries, they 62: cannot be made whole (or treated as whole) without 62: you providing a run input file. 62: 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: Selected 0: 'System' 62: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 62: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (48 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 37 tests from 10 test suites ran. (3282 ms total) 62: [ PASSED ] 37 tests. 62/104 Test #62: GmxAnaTest ................................ Passed 3.32 sec test 63 Start 63: GmxPreprocessTests 63: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests 63: Test timeout computed to be: 1920 63: [==========] Running 237 tests from 16 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertInteractionsTest 63: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 63: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 63: [----------] 1 test from ConvertInteractionsTest (0 ms total) 63: 63: [----------] 5 tests from GenconfTest 63: [ RUN ] GenconfTest.nbox_Works 63: [ OK ] GenconfTest.nbox_Works (2 ms) 63: [ RUN ] GenconfTest.nbox_norenumber_Works 63: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 63: [ RUN ] GenconfTest.nbox_dist_Works 63: [ OK ] GenconfTest.nbox_dist_Works (2 ms) 63: [ RUN ] GenconfTest.nbox_rot_Works 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: center of geometry: 1.733667, 1.477000, 0.905167 63: [ OK ] GenconfTest.nbox_rot_Works (4 ms) 63: [ RUN ] GenconfTest.trj_Works 63: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 63: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Last frame 3 time 3.000 63: [ OK ] GenconfTest.trj_Works (1 ms) 63: [----------] 5 tests from GenconfTest (11 ms total) 63: 63: [----------] 2 tests from GenionTest 63: [ RUN ] GenionTest.HighConcentrationIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Group 0 ( System) has 653 elements 63: Group 1 ( Water) has 648 elements 63: Group 2 ( SOL) has 648 elements 63: Group 3 ( non-Water) has 5 elements 63: Group 4 ( Other) has 5 elements 63: Group 5 ( METH) has 5 elements 63: Select a group: Number of (3-atomic) solvent molecules: 216 63: Using random seed 1997. 63: Replacing solvent molecule 56 (atom 168) with NA 63: Replacing solvent molecule 120 (atom 360) with NA 63: Replacing solvent molecule 182 (atom 546) with NA 63: Replacing solvent molecule 71 (atom 213) with NA 63: Replacing solvent molecule 189 (atom 567) with CL 63: Replacing solvent molecule 54 (atom 162) with CL 63: Replacing solvent molecule 155 (atom 465) with CL 63: Replacing solvent molecule 99 (atom 297) with CL 63: 63: Setting the LD random seed to -67832437 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: Will try to add 4 NA ions and 4 CL ions. 63: Select a continuous group of solvent molecules 63: Selected 1: 'Water' 63: [ OK ] GenionTest.HighConcentrationIonPlacement (423 ms) 63: [ RUN ] GenionTest.NoIonPlacement 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 63: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 63: on the accuracy of your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 63: buffer. The cluster pair list does have a buffering effect, but choosing 63: a larger rlist might be necessary for good energy conservation. 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 63: < 0 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 1308.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.3-Debian_1 (double precision) 63: No ions to add, will just copy input configuration. 63: Setting the LD random seed to -24658436 63: 63: Generated 331705 of the 331705 non-bonded parameter combinations 63: 63: Generated 331705 of the 331705 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Excluding 3 bonded neighbours molecule type 'methane' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216_with_methane.gro' 63: Analysing residue names: 63: There are: 216 Water residues 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GenionTest.NoIonPlacement (484 ms) 63: [----------] 2 tests from GenionTest (908 ms total) 63: 63: [----------] 1 test from GenRestrTest 63: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 63: 63: Reading structure file 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Select group to position restrain 63: Selected 3: 'C-alpha' 63: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 63: [----------] 1 test from GenRestrTest (1 ms total) 63: 63: [----------] 9 tests from PreprocessingAtomTypesTest 63: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 63: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 63: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 63: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 63: 63: [----------] 10 tests from PreprocessingBondAtomTypeTest 63: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 63: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 63: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 63: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 63: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 63: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 63: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 63: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 63: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 63: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 63: 63: [----------] 3 tests from GromppDirectiveTest 63: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -37749789 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1073759489 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (9 ms) 63: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 63: coefficients that do not sum to zero. This does not affect the simulation 63: and can be ignored, unless you are comparing potential energy values with 63: other force field ports and/or MD software. 63: First such dihedral in molecule A, involving atoms 0 2 1 3 63: 63: 63: NOTE 2 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -1813253186 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -71319585 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (3 ms) 63: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 63: Setting the LD random seed to -1465913378 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1786798174 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (13 ms) 63: [----------] 3 tests from GromppDirectiveTest (29 ms total) 63: 63: [----------] 6 tests from InsertMoleculesTest 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: 63: Added 1 molecules (out of 1 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 63: 63: Output configuration contains 8 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (9 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 success (now 6 atoms)! 63: Try 4 success (now 8 atoms)! 63: Try 5 success (now 10 atoms)! 63: 63: Added 5 molecules (out of 5 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 63: 63: Output configuration contains 10 atoms in 10 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (4 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 8 atoms)! 63: Try 2 success (now 10 atoms)! 63: 63: Added 2 molecules (out of 2 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 63: 63: Output configuration contains 10 atoms in 4 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (2 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 63: Reading solute configuration 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Try 1 success (now 650 atoms)! 63: Try 2 success (now 652 atoms)! 63: Try 3 success (now 654 atoms)! 63: Try 4 success (now 656 atoms)! 63: 63: Added 4 molecules (out of 4 requested) 63: Replaced 8 residues (24 atoms) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 63: 63: Output configuration contains 632 atoms in 212 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (5 ms) 63: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Using random seed 1997 63: Read 4 positions from file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 63: 63: Try 1 success (now 2 atoms)! 63: Try 2 success (now 4 atoms)! 63: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 63: Try 13 success (now 6 atoms)! 63: 63: Added 3 molecules (out of 4 requested) 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 63: 63: Output configuration contains 6 atoms in 3 residues 63: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (4 ms) 63: [----------] 6 tests from InsertMoleculesTest (26 ms total) 63: 63: [----------] 3 tests from MassRepartitioning 63: [ RUN ] MassRepartitioning.ValidCaseWorks 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 63: [ RUN ] MassRepartitioning.UnboundGivesWarning 63: 63: WARNING 1 [file unknown]: 63: The are 1 atoms that have a mass below the mass repartitioning limit but 63: are not bound. These masses cannot be repartitioned. 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 63: [ RUN ] MassRepartitioning.LightPartnerGivesError 63: 63: ERROR 1 [file unknown]: 63: Light atoms are bound to at least one atom that has a too low mass for 63: repartitioning 63: 63: The smallest mass in the system is 2, setting the minimum mass to 6 63: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 63: [----------] 3 tests from MassRepartitioning (0 ms total) 63: 63: [----------] 36 tests from GetIrTest 63: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 63: Ignoring obsolete mdp entry 'title' 63: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (7 ms) 63: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 63: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (8 ms) 63: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) 63: [ RUN ] GetIrTest.RejectsValueWithoutKey 63: [ OK ] GetIrTest.RejectsValueWithoutKey (5 ms) 63: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 63: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (4 ms) 63: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (3 ms) 63: [ RUN ] GetIrTest.AcceptsEmptyLines 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsEmptyLines (3 ms) 63: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstenergy 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstpcouple 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 63: Pressure coupling incorrect number of values (I need exactly 1) 63: 63: 63: ERROR 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: With multiple time stepping, nstpcouple should be a multiple of 63: mts-factor 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: The Berendsen barostat does not generate any strictly correct ensemble, 63: and should not be used for new production simulations (in our opinion). 63: We recommend using the C-rescale barostat instead. 63: 63: 63: ERROR 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 63: compressibility must be > 0 when using pressure coupling Berendsen 63: 63: 63: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 63: [ RUN ] GetIrTest.MtsCheckNstdhdl 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstdhdl (5) 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: ERROR 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 63: Lambda state must be set, either with init-lambda-state or with 63: init-lambda 63: 63: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 63: [ RUN ] GetIrTest.MtsCheckSDNotSupported 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: Multiple time stepping is only supported with integrator md 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MtsCheckSDNotSupported (13 ms) 63: [ RUN ] GetIrTest.AcceptsElectricField 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 63: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 63: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 63: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (8 ms) 63: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsImplicitSolventNo (2 ms) 63: [ RUN ] GetIrTest.RejectsImplicitSolventYes 63: [ OK ] GetIrTest.RejectsImplicitSolventYes (4 ms) 63: [ RUN ] GetIrTest.AcceptsMimic 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsMimic (2 ms) 63: [ RUN ] GetIrTest.AcceptsTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 63: pull-coord2 has a non-zero force constant and is also referenced in 63: pull-coord1-expression. Make sure that this is intended. In most use 63: cases, the pull coordinates referenced by a transformation coordinate 63: should have their force constant set to zero. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsTransformationCoord (5 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 63: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 63: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 63: pull-coord2 can not use pull-coord1 in the transformation since this is a 63: constraint 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (5 ms) 63: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 63: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 63: [ RUN ] GetIrTest.MissingTransformationCoordExpression 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 63: pull-coord1-expression not set for pull coordinate of geometry 63: 'transformation' 63: 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.MissingTransformationCoordExpression (6 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (5 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 63: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 63: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 63: in total 100001 steps. This is not compatible with using soft-core 63: potentials. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (5 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 63: won't change anymore after step 100000 until the end of the simulation 63: after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 63: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (11 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 63: 63: ERROR 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 63: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 63: components won't change anymore after step 100000 until the end of the 63: simulation after 100001 steps. 63: 63: 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 63: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 63: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 63: [ RUN ] GetIrTest.AcceptsFmmOptions 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsFmmOptions_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: [ OK ] GetIrTest.AcceptsFmmOptions (8 ms) 63: [----------] 36 tests from GetIrTest (155 ms total) 63: 63: [----------] 6 tests from SolvateTest 63: [ RUN ] SolvateTest.cs_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 1x1x1 boxes 63: Solvent box contains 270 atoms in 90 residues 63: Removed 129 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 47 residues 63: Generated solvent containing 141 atoms in 47 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 63: 63: Output configuration contains 141 atoms in 47 residues 63: Volume : 1.331 (nm^3) 63: Density : 1056.36 (g/l) 63: Number of solvent molecules: 47 63: 63: [ OK ] SolvateTest.cs_box_Works (3 ms) 63: [ RUN ] SolvateTest.cs_cp_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: [ OK ] SolvateTest.cs_cp_Works (28 ms) 63: [ RUN ] SolvateTest.cs_cp_p_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 886 residues 63: Generated solvent containing 2658 atoms in 886 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 63: 63: Output configuration contains 2664 atoms in 888 residues 63: Volume : 27.2709 (nm^3) 63: Density : 974.777 (g/l) 63: Number of solvent molecules: 886 63: 63: Processing topology 63: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 63: [ OK ] SolvateTest.cs_cp_p_Works (27 ms) 63: [ RUN ] SolvateTest.shell_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 3660 atoms in 1220 residues 63: Removed 987 solvent atoms due to solvent-solvent overlap 63: Removed 1902 solvent atoms more than 1.000000 nm from solute. 63: Removed 15 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 252 residues 63: Generated solvent containing 756 atoms in 252 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 63: 63: Output configuration contains 762 atoms in 254 residues 63: Volume : 27.2709 (nm^3) 63: Density : 279.3 (g/l) 63: Number of solvent molecules: 252 63: 63: [ OK ] SolvateTest.shell_Works (13 ms) 63: [ RUN ] SolvateTest.update_Topology_Works 63: Reading solute configuration 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 3x3x3 boxes 63: Solvent box contains 14952 atoms in 4984 residues 63: Removed 2787 solvent atoms due to solvent-solvent overlap 63: Removed 30 solvent atoms due to solute-solvent overlap 63: Sorting configuration 63: Found 2 different molecule types: 63: HOH ( 3 atoms): 1876 residues 63: SOL ( 3 atoms): 2169 residues 63: Generated solvent containing 0 atoms in 0 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 63: 63: Output configuration contains 12141 atoms in 4047 residues 63: Volume : 125 (nm^3) 63: Density : 968.963 (g/l) 63: Number of solvent molecules: 4045 63: 63: Processing topology 63: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 63: [ OK ] SolvateTest.update_Topology_Works (102 ms) 63: [ RUN ] SolvateTest.cs_pdb_big_box_Works 63: Reading solvent configuration 63: 63: Initialising inter-atomic distances... 63: 63: WARNING: Masses and atomic (Van der Waals) radii will be guessed 63: based on residue and atom names, since they could not be 63: definitively assigned from the information in your input 63: files. These guessed numbers might deviate from the mass 63: and radius of the atom type. Please check the output 63: files if necessary. Note, that this functionality may 63: be removed in a future GROMACS version. Please, consider 63: using another file format for your input. 63: 63: The atomic radii are set according to: 63: 63: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 63: A. Bondi 63: van der Waals Volumes and Radii 63: J. Phys. Chem. (1964) 63: https://doi.org/10.1021/j100785a001 63: -------- -------- --- Thank You --- -------- -------- 63: 63: Generating solvent configuration 63: Will generate new solvent configuration of 2x2x2 boxes 63: Solvent box contains 1218 atoms in 406 residues 63: Removed 555 solvent atoms due to solvent-solvent overlap 63: Sorting configuration 63: Found 1 molecule type: 63: SOL ( 3 atoms): 221 residues 63: Generated solvent containing 663 atoms in 221 residues 63: Writing generated configuration to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 63: 63: Output configuration contains 663 atoms in 221 residues 63: Volume : 8 (nm^3) 63: Density : 826.409 (g/l) 63: Number of solvent molecules: 221 63: 63: [ OK ] SolvateTest.cs_pdb_big_box_Works (15 ms) 63: [----------] 6 tests from SolvateTest (191 ms total) 63: 63: [----------] 1 test from TopDirTests 63: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 63: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 63: [----------] 1 test from TopDirTests (0 ms total) 63: 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 63: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 63: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 63: Skipping interaction type that does not represent a interaction with parameters converted in grompp 63: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 63: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (8 ms total) 63: 63: [----------] 16 tests from CorrectVelocity/MaxwellTest 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (3 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (1 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 63: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 63: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (1 ms) 63: [----------] 16 tests from CorrectVelocity/MaxwellTest (43 ms total) 63: 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -60871735 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -25199121 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -556009474 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2144337653 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 (7 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -37749259 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 654219671 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 (7 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -1859588 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1999339507 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 (14 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -268456193 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1820180376 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 (5 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -536887629 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -35137796 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 (5 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to 1872494335 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -155320713 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 (4 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -1079542018 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1620064513 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to 1978293023 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -609255585 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 (5 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -136578131 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to 2146556671 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -76548881 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1075978305 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 (6 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to 468581375 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2079850367 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 (5 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -269484625 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1082787462 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 (10 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to 1610444271 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1898221643 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 (43 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -51077637 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1209012861 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 (7 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -38285591 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -4491274 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 (11 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -1208158285 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -1073743511 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 (3 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to 1911418863 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 783940601 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 (7 ms) 63: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives.top, line 102]: 63: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 21.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.tpr, VERSION 2026.3-Debian_1 (double precision) 63: Setting the LD random seed to -1627965915 63: 63: Generated 10 of the 10 non-bonded parameter combinations 63: 63: Generated 10 of the 10 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 63: 63: Setting gen_seed to -94643425 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 (3 ms) 63: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest (163 ms total) 63: 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 63: Setting the LD random seed to -1084227617 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (37 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 63: Setting the LD random seed to -604135430 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (10 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -1242599554 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1979703033 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (13 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to 1064828917 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -4202536 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (2 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to 669433575 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1559941117 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (5 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -84152418 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1243611682 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (9 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 63: Setting the LD random seed to -1610655270 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (13 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 63: Setting the LD random seed to -33620004 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1611276833 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (12 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 63: Setting the LD random seed to -1678049281 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (13 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 63: Setting the LD random seed to -134217731 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1749041665 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (16 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 63: Setting the LD random seed to 2046808023 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2146754547 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (13 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 63: Setting the LD random seed to -807634984 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -539276547 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (14 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 63: Setting the LD random seed to -878968833 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -696258789 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (7 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 63: Setting the LD random seed to -34682627 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1189165569 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (14 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 63: Setting the LD random seed to -554369181 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 1979643802 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (19 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 63: Setting the LD random seed to -1411449993 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -423674401 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (12 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -134223121 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -266244 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (11 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -536892545 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to 2138898365 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (27 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 63: Setting the LD random seed to 1330559487 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (13 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 63: Setting the LD random seed to 2138561535 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -155681 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (15 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 63: Setting the LD random seed to -42217985 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (11 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 63: Ignoring obsolete mdp entry 'title' 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 1 [file directives-cmap.top, line 121]: 63: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 63: any other atom in the same moleculetype. Although technically this might 63: not cause issues in a simulation, this often means that the user forgot 63: to add a bond/potential/constraint or put multiple molecules in the same 63: moleculetype definition by mistake. Run with -v to get information for 63: each atom. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 63: NVE simulation: will use the initial temperature of 300.000 K for 63: determining the Verlet buffer size 63: 63: 63: There were 2 NOTEs 63: Setting the LD random seed to -645990529 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -471019525 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: Analysing residue names: 63: There are: 1 Other residues 63: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (3 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 63: Setting the LD random seed to -176961033 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (15 ms) 63: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 63: Setting the LD random seed to 2125426172 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 0 bonded neighbours molecule type 'A' 63: 63: Setting gen_seed to -1515192578 63: 63: Velocities were taken from a Maxwell distribution at 300 K 63: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 (20 ms) 63: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest (354 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 237 tests from 16 test suites ran. (1896 ms total) 63: [ PASSED ] 197 tests. 63: [ SKIPPED ] 40 tests, listed below: 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 63: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 63/104 Test #63: GmxPreprocessTests ........................ Passed 1.94 sec test 64 Start 64: Pdb2gmx1Test 64: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 64: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests 64: Test timeout computed to be: 1920 64: [==========] Running 30 tests from 1 test suite. 64: [----------] Global test environment set-up. 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (122 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (48 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (33 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (78 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (29 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (61 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (47 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (33 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip3p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (99 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (48 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (35 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (38 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (99 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (41 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (54 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip4p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (115 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 0 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 0 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (40 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 0 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (50 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 0 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (40 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 0 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (97 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: Marked 124 virtual sites 64: Added 16 dummy masses 64: Added 26 new constraints 64: Before cleaning: 653 pairs 64: Before cleaning: 663 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 252 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 254, now 254 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 663 dihedrals, 51 impropers, 457 angles 64: 650 pairs, 254 bonds and 130 virtual sites 64: 64: Total mass 1846.112 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (49 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: Marked 132 virtual sites 64: Added 10 dummy masses 64: Added 19 new constraints 64: Before cleaning: 748 pairs 64: Before cleaning: 778 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 281 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 290, now 290 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 778 dihedrals, 72 impropers, 516 angles 64: 736 pairs, 290 bonds and 133 virtual sites 64: 64: Total mass 2088.357 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: Marked 123 virtual sites 64: Added 22 dummy masses 64: Added 35 new constraints 64: Before cleaning: 676 pairs 64: Before cleaning: 696 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 255 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 261, now 261 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 696 dihedrals, 56 impropers, 472 angles 64: 667 pairs, 261 bonds and 132 virtual sites 64: 64: Total mass 1861.128 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (38 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: Marked 111 virtual sites 64: Added 18 dummy masses 64: Added 31 new constraints 64: Before cleaning: 603 pairs 64: Before cleaning: 618 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: PRO-COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 228 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 232, now 232 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 618 dihedrals, 48 impropers, 419 angles 64: 597 pairs, 232 bonds and 116 virtual sites 64: 64: Total mass 1662.883 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 64: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/oplsaa.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: Marked 447 virtual sites 64: Added 58 dummy masses 64: Added 101 new constraints 64: Before cleaning: 2499 pairs 64: Before cleaning: 2524 dihedrals 64: Using the Oplsaa force field in directory oplsaa.ff 64: 64: going to rename oplsaa.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Oplsaa) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 936 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 951, now 951 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 2524 dihedrals, 208 impropers, 1704 angles 64: 2469 pairs, 951 bonds and 462 virtual sites 64: 64: Total mass 6908.578 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Oplsaa force field and the tip5p water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (103 ms) 64: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1725 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 30 tests from 1 test suite ran. (1725 ms total) 64: [ PASSED ] 30 tests. 64/104 Test #64: Pdb2gmx1Test .............................. Passed 1.76 sec test 65 Start 65: Pdb2gmx2Test 65: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 65: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests 65: Test timeout computed to be: 1920 65: [==========] Running 40 tests from 2 test suites. 65: [----------] Global test environment set-up. 65: [----------] 20 tests from G43a1/Pdb2gmxTest 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (60 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (49 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (38 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (86 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (63 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (73 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (57 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (45 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (49 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (34 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (81 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 37 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 305 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 165 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 172, now 167 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 77 impropers, 241 angles 65: 267 pairs, 167 bonds and 37 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (41 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 53 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 429 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 202 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 216, now 211 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 134 impropers, 316 angles 65: 273 pairs, 211 bonds and 51 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (46 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 36 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 349 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 168 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 179, now 174 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 102 impropers, 260 angles 65: 242 pairs, 174 bonds and 36 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (54 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 33 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 299 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 150 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 159, now 154 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 80 impropers, 227 angles 65: 232 pairs, 154 bonds and 31 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (64 ms) 65: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos43a1.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 146 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1256 dihedrals 65: Using the Gromos43a1 force field in directory gromos43a1.ff 65: 65: going to rename gromos43a1.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos43a1) 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 635 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 655, now 650 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 350 impropers, 955 angles 65: 972 pairs, 650 bonds and 137 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos43a1 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (56 ms) 65: [----------] 20 tests from G43a1/Pdb2gmxTest (1116 ms total) 65: 65: [----------] 20 tests from G53a6/Pdb2gmxTest 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (54 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (32 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (50 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (44 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (33 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (54 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (48 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (45 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (75 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 0 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (48 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (62 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 0 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (43 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 0 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 0 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (92 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 39 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 267 pairs 65: Before cleaning: 312 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 167 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 174, now 169 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 90 dihedrals, 79 impropers, 245 angles 65: 267 pairs, 169 bonds and 39 virtual sites 65: 65: Total mass 1846.116 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (66 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 57 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 273 pairs 65: Before cleaning: 443 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 206 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 220, now 215 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 93 dihedrals, 138 impropers, 324 angles 65: 273 pairs, 215 bonds and 55 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (76 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 38 virtual sites 65: Added 4 dummy masses 65: Added 8 new constraints 65: 65: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 242 pairs 65: Before cleaning: 356 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 170 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 181, now 176 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 81 dihedrals, 104 impropers, 264 angles 65: 242 pairs, 176 bonds and 38 virtual sites 65: 65: Total mass 1861.132 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (54 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 35 virtual sites 65: Added 4 dummy masses 65: Added 10 new constraints 65: 65: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 232 pairs 65: Before cleaning: 306 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 152 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 161, now 156 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 78 dihedrals, 82 impropers, 231 angles 65: 232 pairs, 156 bonds and 33 virtual sites 65: 65: Total mass 1662.887 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (49 ms) 65: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.rtp 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/gromos53a6.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: 65: WARNING: Duplicate line found in or between hackblock and rtp entries 65: 65: Marked 150 virtual sites 65: Added 10 dummy masses 65: Added 29 new constraints 65: 65: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom H used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: 65: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 65: to an entry in the topology database, but the atom O used in 65: an interaction of type angle in that entry is not found in the 65: input file. Perhaps your atom and/or residue naming needs to be 65: fixed. 65: 65: 65: Before cleaning: 972 pairs 65: Before cleaning: 1270 dihedrals 65: Using the Gromos53a6 force field in directory gromos53a6.ff 65: 65: going to rename gromos53a6.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Gromos53a6) 65: 65: Using default: not generating all possible dihedrals 65: 65: Using default: excluding 3 bonded neighbors 65: 65: Using default: generating 1,4 H--H interactions 65: 65: Using default: removing proper dihedrals found on the same bond as a proper dihedral 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 639 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 659, now 654 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 321 dihedrals, 354 impropers, 963 angles 65: 972 pairs, 654 bonds and 141 virtual sites 65: 65: Total mass 6908.582 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Gromos53a6 force field and the spce water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (94 ms) 65: [----------] 20 tests from G53a6/Pdb2gmxTest (1176 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 40 tests from 2 test suites ran. (2293 ms total) 65: [ PASSED ] 40 tests. 65/104 Test #65: Pdb2gmx2Test .............................. Passed 2.32 sec test 66 Start 66: Pdb2gmx3Test 66: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 66: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/gmxpreprocess/tests 66: Test timeout computed to be: 1920 66: [==========] Running 55 tests from 9 test suites. 66: [----------] Global test environment set-up. 66: [----------] 10 tests from Amber/Pdb2gmxTest 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (57 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (50 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (46 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (44 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (116 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 691 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 255, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 691 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (63 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 788 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 291, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 788 dihedrals, 72 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (53 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 727 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 262, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 727 dihedrals, 56 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (41 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 634 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 233, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 634 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) 66: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2631 dihedrals 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 952, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2631 dihedrals, 208 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber99sb-ildn force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (78 ms) 66: [----------] 10 tests from Amber/Pdb2gmxTest (599 ms total) 66: 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest 66: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber99sb-ildn.ff/rna.arn 66: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 66: 66: going to rename amber99sb-ildn.ff/aminoacids.r2b 66: 66: going to rename amber99sb-ildn.ff/dna.r2b 66: 66: going to rename amber99sb-ildn.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber99sb-ildn) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber99sb-ildn force field and the tip4p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (21 ms) 66: [----------] 1 test from AmberTip4p/Pdb2gmxTest (26 ms total) 66: 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (33 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (33 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (101 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 663 dihedrals, 51 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.132 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (39 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 778 dihedrals, 76 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.366 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 696 dihedrals, 58 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.124 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (39 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 618 dihedrals, 48 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.888 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (34 ms) 66: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber14sb.ff/aminoacids.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Amber14sb force field in directory amber14sb.ff 66: 66: going to rename amber14sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber14sb) 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2524 dihedrals, 210 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.576 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Amber14sb force field and the opc3 water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (79 ms) 66: [----------] 10 tests from Amber14Sb/Pdb2gmxTest (462 ms total) 66: 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the opc water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (23 ms) 66: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber19sb.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Using the Amber19sb force field in directory amber19sb.ff 66: 66: going to rename amber19sb.ff/aminoacids.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 66: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 2 4 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber19sb) 66: 66: Processing chain 1 (4 atoms, 2 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 2 residues with 8 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4, now 4 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 2 angles 66: 0 pairs, 4 bonds and 0 virtual sites 66: 66: Total mass 36.032 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 66: 66: The Amber19sb force field and the tip4pew water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (12 ms) 66: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest (41 ms total) 66: 66: [----------] 12 tests from Charmm/Pdb2gmxTest 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 0 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (77 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 0 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (49 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 0 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (40 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 0 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (35 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 0 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (115 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 0 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (13 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 124 virtual sites 66: Added 16 dummy masses 66: Added 26 new constraints 66: Before cleaning: 653 pairs 66: Before cleaning: 663 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 128 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (128 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 252 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 254, now 254 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 663 dihedrals, 48 impropers, 457 angles 66: 650 pairs, 254 bonds and 130 virtual sites 66: 66: Total mass 1846.115 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/A.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (41 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 30 donors and 22 acceptors were found. 66: There are 36 hydrogen bonds 66: Will use HISE for residue 29 66: Will use HISE for residue 32 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS27 HIS29 66: SG90 NE2111 66: HIS29 NE2111 0.987 66: HIS32 NE2135 1.590 1.155 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 132 virtual sites 66: Added 10 dummy masses 66: Added 19 new constraints 66: Before cleaning: 748 pairs 66: Before cleaning: 778 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb... 66: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 149 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (149 atoms, 16 residues) 66: 66: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue PHE33 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus PHE-33: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 281 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 290, now 290 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 778 dihedrals, 49 impropers, 516 angles 66: 736 pairs, 290 bonds and 133 virtual sites 66: 66: Total mass 2088.361 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/B.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (35 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 22 acceptors were found. 66: There are 26 hydrogen bonds 66: Will use HISE for residue 45 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS45 66: NE295 66: MET46 SD102 1.078 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 123 virtual sites 66: Added 22 dummy masses 66: Added 35 new constraints 66: Before cleaning: 676 pairs 66: Before cleaning: 696 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb... 66: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (132 atoms, 16 residues) 66: 66: Identified residue ALA34 as a starting terminus. 66: 66: Identified residue ALA49 as a ending terminus. 66: Start terminus ALA-34: NH3+ 66: End terminus ALA-49: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 261, now 261 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 696 dihedrals, 39 impropers, 472 angles 66: 667 pairs, 261 bonds and 132 virtual sites 66: 66: Total mass 1861.130 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/C.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (38 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 22 donors and 21 acceptors were found. 66: There are 30 hydrogen bonds 66: Will use HISE for residue 60 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS60 66: NE285 66: CYS62 SG98 0.803 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 111 virtual sites 66: Added 18 dummy masses 66: Added 31 new constraints 66: Before cleaning: 603 pairs 66: Before cleaning: 618 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb... 66: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 66: 66: chain #res #atoms 66: 66: 1 ' ' 16 117 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 (117 atoms, 16 residues) 66: 66: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 66: 66: Identified residue LYS50 as a starting terminus. 66: 66: Identified residue PRO65 as a ending terminus. 66: Start terminus LYS-50: NH3+ 66: End terminus PRO-65: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 228 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 232, now 232 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 14 cmap torsion pairs 66: 66: There are 618 dihedrals, 38 impropers, 419 angles 66: 597 pairs, 232 bonds and 116 virtual sites 66: 66: Total mass 1662.885 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/D.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (33 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 89 donors and 98 acceptors were found. 66: There are 129 hydrogen bonds 66: Will use HISE for residue 31 66: Will use HISE for residue 51 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS25 HIS31 HIS51 66: SG14 NE264 NE2226 66: HIS31 NE264 1.921 66: HIS51 NE2226 1.498 2.650 66: CYS80 SG477 0.207 1.984 1.570 66: Linking CYS-25 SG-14 and CYS-80 SG-477... 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 447 virtual sites 66: Added 58 dummy masses 66: Added 101 new constraints 66: Before cleaning: 2499 pairs 66: Before cleaning: 2524 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb... 66: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 58 488 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (488 atoms, 58 residues) 66: 66: Identified residue ASN24 as a starting terminus. 66: 66: Identified residue ARG81 as a ending terminus. 66: Start terminus ASN-24: NH3+ 66: End terminus ARG-81: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 58 residues with 936 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 951, now 951 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 56 cmap torsion pairs 66: 66: There are 2524 dihedrals, 149 impropers, 1704 angles 66: 2469 pairs, 951 bonds and 462 virtual sites 66: 66: Total mass 6908.566 a.m.u. 66: 66: Total charge -6.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/E.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (79 ms) 66: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Marked 8 virtual sites 66: Added 2 dummy masses 66: Added 3 new constraints 66: Before cleaning: 39 pairs 66: Before cleaning: 39 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb... 66: Read 'GLU', 9 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 66: 66: chain #res #atoms 66: 66: 1 'X' 1 9 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'X' (9 atoms, 1 residues) 66: 66: Identified residue GLU1 as a starting terminus. 66: 66: Identified residue GLU1 as a ending terminus. 66: Start terminus GLU-1: NH3+ 66: End terminus GLU-1: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 1 residues with 18 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 17, now 17 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 39 dihedrals, 2 impropers, 30 angles 66: 39 pairs, 17 bonds and 9 virtual sites 66: 66: Total mass 146.123 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/monomer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (19 ms) 66: [----------] 12 tests from Charmm/Pdb2gmxTest (603 ms total) 66: 66: [----------] 8 tests from ChainSep/Pdb2gmxTest 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (38 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 7 acceptors were found. 66: There are 7 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: HIS8 66: NE223 66: MET12 SD55 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 317 pairs 66: Before cleaning: 322 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 7 58 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (58 atoms, 7 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 124 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 125, now 125 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 5 cmap torsion pairs 66: 66: There are 322 dihedrals, 19 impropers, 227 angles 66: 314 pairs, 125 bonds and 0 virtual sites 66: 66: Total mass 846.083 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 124 atoms 7 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (39 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 651 pairs 66: Before cleaning: 661 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 258 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 258, now 258 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 10 cmap torsion pairs 66: 66: There are 661 dihedrals, 46 impropers, 463 angles 66: 648 pairs, 258 bonds and 0 virtual sites 66: 66: Total mass 1882.146 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (42 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 10 donors and 12 acceptors were found. 66: There are 13 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 66: SG9 66: HIS8 NE251 1.055 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 288 pairs 66: Before cleaning: 293 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 8 61 66: 66: 2 'B' 3 25 66: 66: 3 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (61 atoms, 8 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 8 residues with 114 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 115, now 115 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6 cmap torsion pairs 66: 66: There are 293 dihedrals, 23 impropers, 203 angles 66: 285 pairs, 115 bonds and 0 virtual sites 66: 66: Total mass 888.952 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 114 atoms 8 residues 66: 66: Including chain 2 in system: 61 atoms 3 residues 66: 66: Including chain 3 in system: 83 atoms 5 residues 66: 66: Now there are 258 atoms and 16 residues 66: 66: Total mass in system 1882.146 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (38 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 650 pairs 66: Before cleaning: 660 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 3 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 261 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 260, now 260 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 8 cmap torsion pairs 66: 66: There are 660 dihedrals, 45 impropers, 466 angles 66: 647 pairs, 260 bonds and 0 virtual sites 66: 66: Total mass 1900.162 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (29 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 123 pairs 66: Before cleaning: 123 dihedrals 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 6 donors and 4 acceptors were found. 66: There are 3 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 164 pairs 66: Before cleaning: 169 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 152 pairs 66: Before cleaning: 152 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 4 28 66: 66: 2 'B' 4 33 66: 66: 3 'B' 3 25 66: 66: 4 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (28 atoms, 4 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue GLU5 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus GLU-5: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 51 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 50, now 50 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 123 dihedrals, 9 impropers, 88 angles 66: 123 pairs, 50 bonds and 0 virtual sites 66: 66: Total mass 434.421 a.m.u. 66: 66: Total charge -2.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (33 atoms, 4 residues) 66: 66: Identified residue PHE6 as a starting terminus. 66: 66: Identified residue ILE9 as a ending terminus. 66: Start terminus PHE-6: NH3+ 66: End terminus ILE-9: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 66 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 67, now 67 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2 cmap torsion pairs 66: 66: There are 169 dihedrals, 13 impropers, 118 angles 66: 161 pairs, 67 bonds and 0 virtual sites 66: 66: Total mass 472.547 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'B' (25 atoms, 3 residues) 66: 66: Identified residue LYS10 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus LYS-10: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 61 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 60, now 60 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 152 dihedrals, 5 impropers, 112 angles 66: 152 pairs, 60 bonds and 0 virtual sites 66: 66: Total mass 391.552 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Processing chain 4 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 51 atoms 4 residues 66: 66: Including chain 2 in system: 66 atoms 4 residues 66: 66: Including chain 3 in system: 61 atoms 3 residues 66: 66: Including chain 4 in system: 83 atoms 5 residues 66: 66: Now there are 261 atoms and 16 residues 66: 66: Total mass in system 1900.162 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (44 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 25 donors and 23 acceptors were found. 66: There are 41 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 652 pairs 66: Before cleaning: 662 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 16 127 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (127 atoms, 16 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 255 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 256, now 256 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 12 cmap torsion pairs 66: 66: There are 662 dihedrals, 47 impropers, 460 angles 66: 649 pairs, 256 bonds and 0 virtual sites 66: 66: Total mass 1864.131 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (51 ms) 66: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: Analysing hydrogen-bonding network for automated assignment of histidine 66: protonation. 14 donors and 15 acceptors were found. 66: There are 20 hydrogen bonds 66: Will use HISE for residue 8 66: 9 out of 9 lines of specbond.dat converted successfully 66: Special Atom Distance matrix: 66: CYS3 HIS8 66: SG9 NE251 66: HIS8 NE251 1.055 66: MET12 SD83 0.763 0.990 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 441 pairs 66: Before cleaning: 446 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 211 pairs 66: Before cleaning: 216 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 66: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 11 86 66: 66: 2 'C' 5 41 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (86 atoms, 11 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue MET12 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus MET-12: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 11 residues with 172 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 173, now 173 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 9 cmap torsion pairs 66: 66: There are 446 dihedrals, 29 impropers, 312 angles 66: 438 pairs, 173 bonds and 0 virtual sites 66: 66: Total mass 1262.488 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'C' (41 atoms, 5 residues) 66: 66: Identified residue ASN13 as a starting terminus. 66: 66: Identified residue SER17 as a ending terminus. 66: Start terminus ASN-13: NH3+ 66: End terminus SER-17: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 83 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 83, now 83 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 3 cmap torsion pairs 66: 66: There are 216 dihedrals, 18 impropers, 148 angles 66: 211 pairs, 83 bonds and 0 virtual sites 66: 66: Total mass 601.643 a.m.u. 66: 66: Total charge 1.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 172 atoms 11 residues 66: 66: Including chain 2 in system: 83 atoms 5 residues 66: 66: Now there are 255 atoms and 16 residues 66: 66: Total mass in system 1864.131 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (21 ms) 66: [----------] 8 tests from ChainSep/Pdb2gmxTest (327 ms total) 66: 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on changing chain id only (ignoring TER records). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (36 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records only (ignoring chain id). 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (23 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (34 ms) 66: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 83 pairs 66: Before cleaning: 83 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 145 pairs 66: Before cleaning: 150 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb... 66: Read 'Fragments of peptides and ions', 47 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records and chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 3 19 66: 66: 2 'B' 3 28 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (19 atoms, 3 residues) 66: 66: Identified residue ALA2 as a starting terminus. 66: 66: Identified residue ASP4 as a ending terminus. 66: Start terminus ALA-2: NH3+ 66: End terminus ASP-4: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 36 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 35, now 35 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 83 dihedrals, 6 impropers, 61 angles 66: 83 pairs, 35 bonds and 0 virtual sites 66: 66: Total mass 306.314 a.m.u. 66: 66: Total charge -1.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'B' (28 atoms, 3 residues) 66: 66: Identified residue THR18 as a starting terminus. 66: 66: Identified residue TRP20 as a ending terminus. 66: Start terminus THR-18: NH3+ 66: End terminus TRP-20: COO- 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 3 residues with 57 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 58, now 58 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 1 cmap torsion pairs 66: 66: There are 150 dihedrals, 5 impropers, 103 angles 66: 142 pairs, 58 bonds and 0 virtual sites 66: 66: Total mass 404.468 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 36 atoms 3 residues 66: 66: Including chain 2 in system: 57 atoms 3 residues 66: 66: Now there are 93 atoms and 6 residues 66: 66: Total mass in system 710.782 a.m.u. 66: 66: Total charge in system -1.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/fragments.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (26 ms) 66: [----------] 4 tests from ChainChanges/Pdb2gmxTest (121 ms total) 66: 66: [----------] 4 tests from Cyclic/Pdb2gmxTest 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 6040 pairs 66: Before cleaning: 6605 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 66: 66: Moved all the water blocks to the end 66: 66: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 71 1527 66: 66: 2 'Q' 71 1527 66: 66: 3 'Q' 7 7 66: 66: 4 ' ' 10 10 (only water) 66: 66: 5 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'Q' (1527 atoms, 71 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 71 residues with 2297 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 2481, now 2481 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 6605 dihedrals, 183 impropers, 4434 angles 66: 5827 pairs, 2481 bonds and 0 virtual sites 66: 66: Total mass 22984.514 a.m.u. 66: 66: Total charge -71.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'Q' (7 atoms, 7 residues) 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 7 residues with 7 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: No bonds 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 0 angles 66: 0 pairs, 0 bonds and 0 virtual sites 66: 66: Total mass 170.135 a.m.u. 66: 66: Total charge 14.000 e 66: 66: Writing topology 66: 66: Processing chain 4 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 5 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain m9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: olecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 2297 atoms 71 residues 66: 66: Including chain 2 in system: 2297 atoms 71 residues 66: 66: Including chain 3 in system: 7 atoms 7 residues 66: 66: Including chain 4 in system: 30 atoms 10 residues 66: 66: Including chain 5 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.563 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (347 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (103 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: WARNING: all CONECT records are ignored 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 12080 pairs 66: Before cleaning: 13210 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 66: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Moved all the water blocks to the end 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 66: 66: chain #res #atoms 66: 66: 1 'P' 149 3061 66: 66: 2 ' ' 10 10 (only water) 66: 66: 3 ' ' 16 16 (only water) 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'P' (3061 atoms, 149 residues) 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Identified residue G1 as a starting terminus. 66: 66: Identified residue U71 as a ending terminus. 66: 66: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 66: 66: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 66: 66: Disabling further notes about ions. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 149 residues with 4601 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 4962, now 4962 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 13210 dihedrals, 366 impropers, 8868 angles 66: 11654 pairs, 4962 bonds and 0 virtual sites 66: 66: Total mass 46139.162 a.m.u. 66: 66: Total charge -128.000 e 66: 66: Writing topology 66: 66: Processing chain 2 (10 atoms, 10 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 10 residues with 30 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 30, now 30 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 30 angles 66: 0 pairs, 30 bonds and 0 virtual sites 66: 66: Total mass 180.154 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Processing chain 3 (16 atoms, 16 residues) 66: 66: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 16 residues with 48 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 48, now 48 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 0 dihedrals, 0 impropers, 48 angles 66: 0 pairs, 48 bonds and 0 virtual sites 66: 66: Total mass 288.246 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Including chain 1 in system: 4601 atoms 149 residues 66: 66: Including chain 2 in system: 30 atoms 10 residues 66: 66: Including chain 3 in system: 48 atoms 16 residues 66: 66: Now there are 4679 atoms and 175 residues 66: 66: Total mass in system 46607.563 a.m.u. 66: 66: Total charge in system -128.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (606 ms) 66: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/lipids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.c.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/charmm27.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Charmm27 force field in directory charmm27.ff 66: 66: going to rename charmm27.ff/aminoacids.r2b 66: 66: going to rename charmm27.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 66: Read 'CARNOCYCLIN-A', 413 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 66: 66: chain #res #atoms 66: 66: 1 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Charmm27) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 60 cmap torsion pairs 66: 66: There are 2325 dihedrals, 137 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.087 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 66: 66: The Charmm27 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (94 ms) 66: [----------] 4 tests from Cyclic/Pdb2gmxTest (1161 ms total) 66: 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 2325 pairs 66: Before cleaning: 2325 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 2 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 5 47 66: 66: 2 'A' 60 413 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'A' (413 atoms, 60 residues) 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 60 residues with 878 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 880, now 880 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2325 dihedrals, 141 impropers, 1614 angles 66: 2319 pairs, 880 bonds and 0 virtual sites 66: 66: Total mass 5866.100 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 86 atoms 5 residues 66: 66: Including chain 2 in system: 878 atoms 60 residues 66: 66: Now there are 964 atoms and 65 residues 66: 66: Total mass in system 6519.802 a.m.u. 66: 66: Total charge in system 4.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file (134 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 188 pairs 66: Before cleaning: 198 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 233 pairs 66: Before cleaning: 243 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: There are 3 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 4 38 66: 66: 2 'E' 5 47 66: 66: 3 'F' 5 47 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (38 atoms, 4 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 4 residues with 72 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 75, now 74 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 198 dihedrals, 18 impropers, 132 angles 66: 185 pairs, 74 bonds and 0 virtual sites 66: 66: Total mass 543.584 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 2 'E' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Processing chain 3 'F' (47 atoms, 5 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 5 residues with 86 atoms 66: Chain time... 66: 66: Making bonds... 66: 66: Number of bonds was 89, now 89 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 243 dihedrals, 23 impropers, 159 angles 66: 230 pairs, 89 bonds and 0 virtual sites 66: 66: Total mass 653.702 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Including chain 1 in system: 72 atoms 4 residues 66: 66: Including chain 2 in system: 86 atoms 5 residues 66: 66: Including chain 3 in system: 86 atoms 5 residues 66: 66: Now there are 244 atoms and 14 residues 66: 66: Total mass in system 1850.988 a.m.u. 66: 66: Total charge in system 0.000 e 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file (51 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 2558 pairs 66: Before cleaning: 2568 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 66: Read 'Two cyclic peptides, one small one big', 460 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 1 places. 66: 66: There are 1 chains and 0 blocks of water and 65 residues with 460 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 65 460 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (460 atoms, 65 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue LEU1 as a starting terminus. 66: 66: Identified residue LEU60 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 65 residues with 964 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 969, now 969 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 2568 dihedrals, 164 impropers, 1773 angles 66: 2549 pairs, 969 bonds and 0 virtual sites 66: 66: Total mass 6519.802 a.m.u. 66: 66: Total charge 4.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file (103 ms) 66: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.r2b 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.r2b 66: All occupancies are one 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/atomtypes.atp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.rtp 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.hdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.n.tdb 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.c.tdb 66: 9 out of 9 lines of specbond.dat converted successfully 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/aminoacids.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/dna.arn 66: Opening force field file /build/reproducible-path/gromacs-2026.3/share/top/amber96.ff/rna.arn 66: Before cleaning: 654 pairs 66: Before cleaning: 684 dihedrals 66: Using the Amber96 force field in directory amber96.ff 66: 66: going to rename amber96.ff/aminoacids.r2b 66: 66: going to rename amber96.ff/dna.r2b 66: 66: going to rename amber96.ff/rna.r2b 66: Reading /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 66: Read 'One linear then two cyclic peptides', 132 atoms 66: 66: Analyzing pdb file 66: Splitting chemical chains based on TER records or chain id changing. 66: 66: Merged chains into joint molecule definitions at 2 places. 66: 66: There are 1 chains and 0 blocks of water and 14 residues with 132 atoms 66: 66: chain #res #atoms 66: 66: 1 'C' 14 132 66: 66: All occupancies are one 66: 66: Reading residue database... (Amber96) 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Preserving residues names by default 66: 66: Processing chain 1 'C' (132 atoms, 14 residues) 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue TRP4 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Identified residue ASN1 as a starting terminus. 66: 66: Identified residue GLN5 as a ending terminus. 66: 66: Checking for duplicate atoms.... 66: 66: Generating any missing hydrogen atoms and/or adding termini. 66: 66: Now there are 14 residues with 244 atoms 66: 66: Making bonds... 66: 66: Number of bonds was 253, now 252 66: 66: Generating angles, dihedrals and pairs... 66: 66: Making cmap torsions... 66: 66: There are 684 dihedrals, 64 impropers, 450 angles 66: 645 pairs, 252 bonds and 0 virtual sites 66: 66: Total mass 1850.988 a.m.u. 66: 66: Total charge 0.000 e 66: 66: Writing topology 66: 66: Writing coordinate file... 66: 66: --------- PLEASE NOTE ------------ 66: 66: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.3/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 66: 66: The Amber96 force field and the tip3p water model are used. 66: 66: --------- ETON ESAELP ------------ 66: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file (43 ms) 66: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest (348 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 55 tests from 9 test suites ran. (3701 ms total) 66: [ PASSED ] 55 tests. 66/104 Test #66: Pdb2gmx3Test .............................. Passed 3.73 sec test 67 Start 67: CorrelationsTest 67: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 67: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/correlationfunctions/tests 67: Test timeout computed to be: 60 67: [==========] Running 21 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 10 tests from AutocorrTest 67: [ RUN ] AutocorrTest.EacNormal 67: [ OK ] AutocorrTest.EacNormal (21 ms) 67: [ RUN ] AutocorrTest.EacNoNormalize 67: [ OK ] AutocorrTest.EacNoNormalize (11 ms) 67: [ RUN ] AutocorrTest.EacCos 67: [ OK ] AutocorrTest.EacCos (18 ms) 67: [ RUN ] AutocorrTest.EacVector 67: [ OK ] AutocorrTest.EacVector (22 ms) 67: [ RUN ] AutocorrTest.EacRcross 67: [ OK ] AutocorrTest.EacRcross (3 ms) 67: [ RUN ] AutocorrTest.EacP0 67: [ OK ] AutocorrTest.EacP0 (20 ms) 67: [ RUN ] AutocorrTest.EacP1 67: [ OK ] AutocorrTest.EacP1 (23 ms) 67: [ RUN ] AutocorrTest.EacP2 67: [ OK ] AutocorrTest.EacP2 (41 ms) 67: [ RUN ] AutocorrTest.EacP3 67: [ OK ] AutocorrTest.EacP3 (10 ms) 67: [ RUN ] AutocorrTest.EacP4 67: [ OK ] AutocorrTest.EacP4 (20 ms) 67: [----------] 10 tests from AutocorrTest (194 ms total) 67: 67: [----------] 10 tests from ExpfitTest 67: [ RUN ] ExpfitTest.EffnEXP1 67: [ OK ] ExpfitTest.EffnEXP1 (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP2 67: [ OK ] ExpfitTest.EffnEXP2 (2 ms) 67: [ RUN ] ExpfitTest.EffnEXPEXP 67: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 67: [ RUN ] ExpfitTest.EffnEXP5 67: [ OK ] ExpfitTest.EffnEXP5 (2 ms) 67: [ RUN ] ExpfitTest.EffnEXP7 67: [ OK ] ExpfitTest.EffnEXP7 (8 ms) 67: [ RUN ] ExpfitTest.EffnEXP9 67: [ OK ] ExpfitTest.EffnEXP9 (6 ms) 67: [ RUN ] ExpfitTest.EffnERF 67: [ OK ] ExpfitTest.EffnERF (1 ms) 67: [ RUN ] ExpfitTest.EffnERREST 67: [ OK ] ExpfitTest.EffnERREST (1 ms) 67: [ RUN ] ExpfitTest.EffnVAC 67: [ OK ] ExpfitTest.EffnVAC (4 ms) 67: [ RUN ] ExpfitTest.EffnPRES 67: [ OK ] ExpfitTest.EffnPRES (7 ms) 67: [----------] 10 tests from ExpfitTest (52 ms total) 67: 67: [----------] 1 test from ManyAutocorrelationTest 67: [ RUN ] ManyAutocorrelationTest.Empty 67: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 67: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 21 tests from 3 test suites ran. (258 ms total) 67: [ PASSED ] 21 tests. 67/104 Test #67: CorrelationsTest .......................... Passed 0.29 sec test 68 Start 68: AnalysisDataUnitTests 68: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/analysisdata/tests 68: Test timeout computed to be: 60 68: [==========] Running 69 tests from 14 test suites. 68: [----------] Global test environment set-up. 68: [----------] 3 tests from AnalysisDataInitializationTest 68: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 68: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 68: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 68: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 68: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/0 (2 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/1 (0 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 68: 68: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 68: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 68: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 68: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 68: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 68: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 68: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 68: 68: [----------] 4 tests from AnalysisArrayDataTest 68: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 68: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms) 68: [ RUN ] AnalysisArrayDataTest.StorageWorks 68: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 68: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 68: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 68: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 68: [----------] 4 tests from AnalysisArrayDataTest (2 ms total) 68: 68: [----------] 6 tests from AverageModuleTest 68: [ RUN ] AverageModuleTest.BasicTest 68: [ OK ] AverageModuleTest.BasicTest (5 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipointData 68: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 68: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 68: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 68: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeXAxis 68: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 68: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 68: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 68: [----------] 6 tests from AverageModuleTest (10 ms total) 68: 68: [----------] 2 tests from FrameAverageModuleTest 68: [ RUN ] FrameAverageModuleTest.BasicTest 68: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 68: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 2 tests from FrameAverageModuleTest (3 ms total) 68: 68: [----------] 7 tests from AnalysisHistogramSettingsTest 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 68: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 68: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 68: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 68: 68: [----------] 2 tests from SimpleHistogramModuleTest 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (2 ms) 68: [----------] 2 tests from SimpleHistogramModuleTest (3 ms total) 68: 68: [----------] 3 tests from WeightedHistogramModuleTest 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 68: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 68: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from WeightedHistogramModuleTest (5 ms total) 68: 68: [----------] 3 tests from BinAverageModuleTest 68: [ RUN ] BinAverageModuleTest.ComputesCorrectly 68: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 68: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 68: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 68: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 68: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 68: [----------] 3 tests from BinAverageModuleTest (2 ms total) 68: 68: [----------] 4 tests from AbstractAverageHistogramTest 68: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 68: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 68: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (2 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 68: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 68: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 68: [----------] 4 tests from AbstractAverageHistogramTest (7 ms total) 68: 68: [----------] 3 tests from LifetimeModuleTest 68: [ RUN ] LifetimeModuleTest.BasicTest 68: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 68: [ RUN ] LifetimeModuleTest.CumulativeTest 68: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 68: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 68: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 68: [----------] 3 tests from LifetimeModuleTest (7 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 69 tests from 14 test suites ran. (51 ms total) 68: [ PASSED ] 69 tests. 68/104 Test #68: AnalysisDataUnitTests ..................... Passed 0.08 sec test 69 Start 69: CoordinateIOTests 69: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/coordinateio/tests 69: Test timeout computed to be: 60 69: [==========] Running 67 tests from 20 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from OutputSelectorDeathTest 69: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (7 ms) 69: [----------] 1 test from OutputSelectorDeathTest (7 ms total) 69: 69: [----------] 5 tests from TrajectoryFrameWriterTest 69: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 69: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (5 ms) 69: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 69: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 69: [----------] 5 tests from TrajectoryFrameWriterTest (8 ms total) 69: 69: [----------] 5 tests from OutputAdapterContainer 69: [ RUN ] OutputAdapterContainer.MakeEmpty 69: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 69: [ RUN ] OutputAdapterContainer.AddAdapter 69: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectBadAdapter 69: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 69: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 69: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 69: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 69: [----------] 5 tests from OutputAdapterContainer (0 ms total) 69: 69: [----------] 3 tests from RegisterFrameConverterTest 69: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 69: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 69: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 69: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 69: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 69: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 69: 69: [----------] 5 tests from FlagTest 69: [ RUN ] FlagTest.CanSetSimpleFlag 69: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 69: [ RUN ] FlagTest.CanAddNewBox 69: [ OK ] FlagTest.CanAddNewBox (0 ms) 69: [ RUN ] FlagTest.SetsImplicitPrecisionChange 69: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitStartTimeChange 69: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 69: [ RUN ] FlagTest.SetsImplicitTimeStepChange 69: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 69: [----------] 5 tests from FlagTest (0 ms total) 69: 69: [----------] 5 tests from SetAtomsTest 69: [ RUN ] SetAtomsTest.RemovesExistingAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 69: [ RUN ] SetAtomsTest.AddsNewAtoms 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 69: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (5 ms) 69: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 69: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 69: [----------] 5 tests from SetAtomsTest (8 ms total) 69: 69: [----------] 2 tests from SetBothTimeTest 69: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 69: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 69: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 69: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 69: [----------] 2 tests from SetBothTimeTest (0 ms total) 69: 69: [----------] 2 tests from SetStartTimeTest 69: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 69: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 69: [ RUN ] SetStartTimeTest.WorksWithZeroStart 69: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 69: [----------] 2 tests from SetStartTimeTest (0 ms total) 69: 69: [----------] 1 test from SetTimeStepTest 69: [ RUN ] SetTimeStepTest.SetTimeStepWorks 69: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 69: [----------] 1 test from SetTimeStepTest (0 ms total) 69: 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (8 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 69: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 69: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (13 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (13 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (14 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (5 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) 69: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) 69: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (12 ms total) 69: 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (2 ms total) 69: 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 69: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 69: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 69: 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 69: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (1 ms total) 69: 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 69: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 69: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 69: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 69: 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 69: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 69: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 67 tests from 20 test suites ran. (78 ms total) 69: [ PASSED ] 67 tests. 69/104 Test #69: CoordinateIOTests ......................... Passed 0.10 sec test 70 Start 70: TrajectoryAnalysisUnitTests 70: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests 70: Test timeout computed to be: 1920 70: [==========] Running 394 tests from 21 test suites. 70: [----------] Global test environment set-up. 70: [----------] 11 tests from AngleModuleTest 70: [ RUN ] AngleModuleTest.ComputesSimpleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesSimpleAngles (4 ms) 70: [ RUN ] AngleModuleTest.ComputesDihedrals 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesDihedrals (5 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPairAngles (6 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (2 ms) 70: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (5 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 70: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system for different angles', 33 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (6 ms) 70: [ RUN ] AngleModuleTest.ComputesMultipleAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.ComputesMultipleAngles (2 ms) 70: [ RUN ] AngleModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesDynamicSelections (2 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (5 ms) 70: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 70: [----------] 11 tests from AngleModuleTest (44 ms total) 70: 70: [----------] 5 tests from ClustsizeTest 70: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 2, cmax: 4, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (4 ms) 70: [ RUN ] ClustsizeTest.NoMolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 70: There is one group in the index 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 24 70: cmid: 1, cmax: 6, max_size: 6 70: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 70: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (3 ms) 70: [ RUN ] ClustsizeTest.MolDefaultCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (14 ms) 70: [ RUN ] ClustsizeTest.MolShortCutoff 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 1, cmax: 6, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (3 ms) 70: [ RUN ] ClustsizeTest.MolCSize 70: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Total number of atoms in clusters = 8 70: cmid: 2, cmax: 4, max_size: 2 70: 50%100%cmid: 2, cmax: 6, max_size: 2 70: 50%100%[ OK ] ClustsizeTest.MolCSize (5 ms) 70: [----------] 5 tests from ClustsizeTest (32 ms total) 70: 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (3 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 8 atoms. 70: Reading frame 0 time 0.000 [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (2 ms) 70: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 70: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 70: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (7 ms total) 70: 70: [----------] 4 tests from ConvertTrjModuleTest 70: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (14 ms) 70: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (7 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (12 ms) 70: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 70: Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (4 ms) 70: [----------] 4 tests from ConvertTrjModuleTest (48 ms total) 70: 70: [----------] 6 tests from DistanceModuleTest 70: [ RUN ] DistanceModuleTest.ComputesDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 70: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2: 70: Number of samples: 5 70: Average distance: 1.43246 nm 70: Standard deviation: 0.96700 nm 70: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 70: Number of samples: 4 70: Average distance: 1.81066 nm 70: Standard deviation: 0.79289 nm 70: [ OK ] DistanceModuleTest.ComputesMultipleDistances (6 ms) 70: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: atomname S1 S2 and res_cog x < 2.8: 70: Number of samples: 3 70: Average distance: 1.72076 nm 70: Standard deviation: 1.24839 nm 70: [ OK ] DistanceModuleTest.HandlesDynamicSelections (6 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: Contacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (5 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: SuccessiveContacts: 70: Number of samples: 2 70: Average distance: 1.00000 nm 70: Standard deviation: 0.00000 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (11 ms) 70: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: ManyContacts: 70: Number of samples: 10 70: Average distance: 1.82913 nm 70: Standard deviation: 0.78478 nm 70: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (9 ms) 70: [----------] 6 tests from DistanceModuleTest (44 ms total) 70: 70: [----------] 2 tests from ExtractClusterModuleTest 70: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 70: trr version: GMX_trn_file (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (7 ms) 70: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 70: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 70: Analyzed 26 frames, last time 0.050 70: There are 8 clusters containing 26 structures, highest framenr is 25 70: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (7 ms) 70: [----------] 2 tests from ExtractClusterModuleTest (15 ms total) 70: 70: [----------] 2 tests from FreeVolumeModuleTest 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for CO2-RM. Set to zero. 70: Could not determine VDW radius for 40 particles. These were set to zero. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 13 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.02 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 70: Fractional free volume 0.194 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (56 ms) 70: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: cutoff = 0.18 nm 70: probe_radius = 0 nm 70: seed = 17 70: ninsert = 1000 probes per nm^3 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 70: Spoel, Luciano T. Costa 70: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 70: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 70: Environ. Sci. Technol. (2013) 70: https://doi.org/10.1021/es4020986 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Free volume 38.48 +/- 0.00 % 70: Total volume 68.92 +/- 0.00 nm^3 70: Number of molecules 340 total mass 63491.38 Dalton 70: Average molar mass: 186.74 Dalton 70: Density rho: 1529.71 +/- 0.00 nm^3 70: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 70: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 70: Fractional free volume 0.200 +/- 0.000 70: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (57 ms) 70: [----------] 2 tests from FreeVolumeModuleTest (114 ms total) 70: 70: [----------] 13 tests from MsdModuleTest 70: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.threeDimensionalDiffusion (10 ms) 70: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 70: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 70: Analyzed 10 frames, last time 9.000 70: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (6 ms) 70: [ RUN ] MsdModuleTest.multipleGroupsWork 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -310415402 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.multipleGroupsWork (36 ms) 70: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 0.100 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 70: Analyzed 21 frames, last time 2.000 70: Setting the LD random seed to -422051843 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (38 ms) 70: [ RUN ] MsdModuleTest.trestartLessThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -674119713 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartLessThanDt (34 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -1073881130 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDt (53 ms) 70: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to 1996488440 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (15 ms) 70: [ RUN ] MsdModuleTest.molTest 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -621811721 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.molTest (16 ms) 70: [ RUN ] MsdModuleTest.beginFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -1346682915 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.beginFit (34 ms) 70: [ RUN ] MsdModuleTest.endFit 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -1082294990 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.endFit (30 ms) 70: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 1818.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: NVE simulation: will use the initial temperature of 288.764 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: NOTE: You provided an index file 70: /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 70: (with -n), but it was not used by any selection. 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 2.000 70: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 70: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 70: Analyzed 21 frames, last time 40.000 70: Setting the LD random seed to -1091797073 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Converted 15 Bonds with virtual sites to connections, 7 left 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (25 ms) 70: [----------] 13 tests from MsdModuleTest (307 ms total) 70: 70: [----------] 9 tests from PairDistanceModuleTest 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistances (13 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (3 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (8 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 70: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (2 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 70: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (7 ms) 70: [----------] 9 tests from PairDistanceModuleTest (42 ms total) 70: 70: [----------] 5 tests from RdfModuleTest 70: [ RUN ] RdfModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.BasicTest (23 ms) 70: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 70: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (11 ms) 70: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (13 ms) 70: [ RUN ] RdfModuleTest.CalculatesSurf 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesSurf (6 ms) 70: [ RUN ] RdfModuleTest.CalculatesXY 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] RdfModuleTest.CalculatesXY (19 ms) 70: [----------] 5 tests from RdfModuleTest (75 ms total) 70: 70: [----------] 5 tests from SasaModuleTest 70: [ RUN ] SasaModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.BasicTest (18 ms) 70: [ RUN ] SasaModuleTest.HandlesSelectedResidues 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesSelectedResidues (8 ms) 70: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (6 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (8 ms) 70: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 70: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 70: of Surface Area and Volume and to Dot Surface Contouring of Molecular 70: Assemblies 70: J. Comp. Chem. (1995) 70: https://doi.org/10.1002/jcc.540160303 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (8 ms) 70: [----------] 5 tests from SasaModuleTest (51 ms total) 70: 70: [----------] 9 tests from SelectModuleTest 70: [ RUN ] SelectModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.BasicTest (4 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (3 ms) 70: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (8 ms) 70: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (2 ms) 70: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (6 ms) 70: [ RUN ] SelectModuleTest.NormalizesSizes 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 70: [ RUN ] SelectModuleTest.WritesResidueNumbers 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 70: [ RUN ] SelectModuleTest.WritesResidueIndices 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 70: [ RUN ] SelectModuleTest.HandlesPrimeInAtomName 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Analyzed topology coordinates 70: [ OK ] SelectModuleTest.HandlesPrimeInAtomName (7 ms) 70: [----------] 9 tests from SelectModuleTest (37 ms total) 70: 70: [----------] 10 tests from SurfaceAreaTest 70: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 70: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 70: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 70: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 70: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints12 70: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints32 70: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints42 70: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 70: [ RUN ] SurfaceAreaTest.SurfacePoints122 70: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 70: [ RUN ] SurfaceAreaTest.Computes100Points 70: [ OK ] SurfaceAreaTest.Computes100Points (2 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 70: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 70: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (3 ms) 70: [----------] 10 tests from SurfaceAreaTest (22 ms total) 70: 70: [----------] 4 tests from TopologyInformation 70: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 70: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 70: [ RUN ] TopologyInformation.WorksWithGroFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithGroFile (0 ms) 70: [ RUN ] TopologyInformation.WorksWithPdbFile 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 70: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file lysozyme.top, line 1465]: 70: System has non-zero total charge: 2.000000 70: Total charge should normally be an integer. See 70: https://manual.gromacs.org/current/user-guide/floating-point.html 70: for discussion on how close it should be to an integer. 70: 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 465.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 70: Setting the LD random seed to -1193312257 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 70: Analysing residue names: 70: There are: 10 Protein residues 70: Analysing Protein... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (297 ms) 70: [----------] 4 tests from TopologyInformation (299 ms total) 70: 70: [----------] 4 tests from TrajectoryModuleTest 70: [ RUN ] TrajectoryModuleTest.BasicTest 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 70: [ RUN ] TrajectoryModuleTest.PlotsXOnly 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.PlotsXOnly (3 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (2 ms) 70: [ RUN ] TrajectoryModuleTest.HandlesNoForces 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from gro file 'Test system', 15 atoms. 70: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 70: Analyzed 2 frames, last time 0.000 70: [ OK ] TrajectoryModuleTest.HandlesNoForces (5 ms) 70: [----------] 4 tests from TrajectoryModuleTest (13 ms total) 70: 70: [----------] 5 tests from UnionFinderTest 70: [ RUN ] UnionFinderTest.WorksEmpty 70: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 70: [ RUN ] UnionFinderTest.BasicMerges 70: [ OK ] UnionFinderTest.BasicMerges (0 ms) 70: [ RUN ] UnionFinderTest.LargerMerges 70: [ OK ] UnionFinderTest.LargerMerges (0 ms) 70: [ RUN ] UnionFinderTest.LongRightMerge 70: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 70: [ RUN ] UnionFinderTest.LongLeftMerge 70: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 70: [----------] 5 tests from UnionFinderTest (0 ms total) 70: 70: [----------] 1 test from MappedUnionFinderTest 70: [ RUN ] MappedUnionFinderTest.BasicMerges 70: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 70: [----------] 1 test from MappedUnionFinderTest (0 ms total) 70: 70: [----------] 192 tests from MoleculeTests/DsspModuleTest 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (34 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (23 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (31 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (33 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (33 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (34 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (32 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (23 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (41 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (32 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (36 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (34 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (35 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (28 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (28 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (23 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (33 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (30 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (30 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (28 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (42 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (34 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (31 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (24 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (24 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (35 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (30 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (30 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (82 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (32 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (28 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (47 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (24 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (58 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (39 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (28 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (30 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (23 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (24 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (29 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (24 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (24 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (23 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (18 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (27 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (23 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (18 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (24 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (18 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (26 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (35 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (36 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (18 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (18 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (18 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (19 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (10 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (15 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (14 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (21 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (16 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (13 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (25 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (20 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (17 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (12 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (11 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (22 ms) 70: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 70: Last frame 0 time 500.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: W. Kabsch, C. Sander 70: Dictionary of protein secondary structure: pattern recognition of 70: hydrogen-bonded and geometrical features 70: Biopolymers (1983) 70: https://doi.org/10.1002/bip.360221211 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 70: Trajectories 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c01344 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (22 ms) 70: [----------] 192 tests from MoleculeTests/DsspModuleTest (4403 ms total) 70: 70: [----------] 3 tests from GyrateTests/GyrateModuleTest 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (15 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (11 ms) 70: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (11 ms) 70: [----------] 3 tests from GyrateTests/GyrateModuleTest (39 ms total) 70: 70: [----------] 96 tests from HBondTests/HbondModuleTest 70: [ RUN ] HBondTests/HbondModuleTest.Works/0 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/0 (28 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/1 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/1 (13 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/2 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/2 (29 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/3 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/3 (13 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/4 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/4 (18 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/5 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/5 (17 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/6 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/6 (19 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/7 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/7 (17 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/8 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/8 (13 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/9 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/9 (14 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/10 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/10 (18 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/11 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/11 (18 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/12 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/12 (23 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/13 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/13 (20 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/14 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/14 (14 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/15 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/15 (17 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/16 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/16 (20 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/17 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/17 (18 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/18 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/18 (19 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/19 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/19 (30 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/20 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/20 (13 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/21 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/21 (19 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/22 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/22 (19 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/23 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/23 (12 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/24 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/24 (19 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/25 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/25 (22 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/26 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/26 (16 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/27 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/27 (16 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/28 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/28 (19 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/29 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/29 (28 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/30 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/30 (16 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/31 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/31 (14 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/32 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/32 (54 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/33 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/33 (81 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/34 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/34 (80 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/35 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/35 (80 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/36 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/36 (87 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/37 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/37 (82 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/38 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/38 (76 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/39 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/39 (50 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/40 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/40 (85 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/41 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/41 (61 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/42 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/42 (48 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/43 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/43 (50 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/44 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/44 (83 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/45 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/45 (100 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/46 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/46 (79 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/47 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/47 (87 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/48 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/48 (46 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/49 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/49 (46 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/50 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/50 (83 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/51 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/51 (75 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/52 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/52 (78 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/53 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/53 (69 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/54 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/54 (53 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/55 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/55 (84 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/56 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/56 (81 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/57 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/57 (77 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/58 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/58 (77 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/59 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/59 (108 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/60 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/60 (97 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/61 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 27 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/61 (46 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/62 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 56 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/62 (86 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/63 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 70: Selection 'Protein' has 29 acceptors and 4 donors. 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Merging hbonds with Acceptor and Donor swapped 70: [ OK ] HBondTests/HbondModuleTest.Works/63 (80 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/64 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/64 (78 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/65 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/65 (78 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/66 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/66 (60 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/67 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/67 (61 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/68 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/68 (81 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/69 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/69 (56 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/70 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/70 (82 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/71 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/71 (80 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/72 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/72 (86 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/73 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/73 (85 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/74 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/74 (85 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/75 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/75 (85 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/76 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/76 (89 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/77 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/77 (84 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/78 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/78 (48 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/79 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/79 (82 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/80 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/80 (79 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/81 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/81 (81 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/82 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/82 (59 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/83 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/83 (79 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/84 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/84 (82 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/85 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/85 (80 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/86 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/86 (81 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/87 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/87 (85 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/88 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/88 (69 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/89 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/89 (48 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/90 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/90 (51 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/91 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/91 (84 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/92 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/92 (53 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/93 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/93 (47 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/94 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/94 (104 ms) 70: [ RUN ] HBondTests/HbondModuleTest.Works/95 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 70: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 70: Analyzed 2 frames, last time 10.000 70: 70: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 70: Selection 'Water' has 1160 acceptors and 1160 donors. 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 70: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 70: Memory Limitation 70: Journal of Chemical Information and Modeling (2024) 70: https://doi.org/10.1021/acs.jcim.3c02087 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] HBondTests/HbondModuleTest.Works/95 (72 ms) 70: [----------] 96 tests from HBondTests/HbondModuleTest (6024 ms total) 70: 70: [----------] 4 tests from MoleculeTests/ScatteringModule 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (13 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (173 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (12 ms) 70: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 70: 70: WARNING: Masses and atomic (Van der Waals) radii will be guessed 70: based on residue and atom names, since they could not be 70: definitively assigned from the information in your input 70: files. These guessed numbers might deviate from the mass 70: and radius of the atom type. Please check the output 70: files if necessary. Note, that this functionality may 70: be removed in a future GROMACS version. Please, consider 70: using another file format for your input. 70: 70: The atomic radii are set according to: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. Bondi 70: van der Waals Volumes and Radii 70: J. Phys. Chem. (1964) 70: https://doi.org/10.1021/j100785a001 70: -------- -------- --- Thank You --- -------- -------- 70: 70: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 70: Last frame 0 time 0.000 70: Analyzed 1 frames, last time 0.000 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 70: Method for calculating small-angle neutron scattering spectra using all-atom 70: molecular dynamics trajectories 70: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 70: https://doi.org/10.1134/S1027451013060372 70: -------- -------- --- Thank You --- -------- -------- 70: 70: 70: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 70: D. T. Cromer, J. B. Mann 70: X-ray scattering factors computed from numerical Hartree-Fock wave functions 70: Acta Cryst. A (1968) 70: https://doi.org/10.1107/S0567739468000550 70: -------- -------- --- Thank You --- -------- -------- 70: 70: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (85 ms) 70: [----------] 4 tests from MoleculeTests/ScatteringModule (288 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 394 tests from 21 test suites ran. (11913 ms total) 70: [ PASSED ] 394 tests. 70/104 Test #70: TrajectoryAnalysisUnitTests ............... Passed 11.95 sec test 71 Start 71: EnergyAnalysisUnitTests 71: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests 71: Test timeout computed to be: 60 71: [==========] Running 12 tests from 5 test suites. 71: [----------] Global test environment set-up. 71: [----------] 2 tests from EnergyTermTest 71: [ RUN ] EnergyTermTest.ConstructWorks 71: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 71: [ RUN ] EnergyTermTest.AddFrameWorks 71: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 71: [----------] 2 tests from EnergyTermTest (0 ms total) 71: 71: [----------] 1 test from DhdlTest 71: [ RUN ] DhdlTest.ExtractDhdl 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 71: Note: file tpx version 110, software tpx version 138 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 71: 71: 71: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 71: [ OK ] DhdlTest.ExtractDhdl (17 ms) 71: [----------] 1 test from DhdlTest (17 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.ExtractOrires 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 71: Reading file /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 71: Note: file tpx version 111, software tpx version 138 71: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 71: End your selection with 0 71: Selecting all 7 orientation restraints 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 71: [ OK ] OriresTest.ExtractOrires (15 ms) 71: [----------] 1 test from OriresTest (15 ms total) 71: 71: [----------] 5 tests from EnergyTest 71: [ RUN ] EnergyTest.ExtractEnergy 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: [ OK ] EnergyTest.ExtractEnergy (9 ms) 71: [ RUN ] EnergyTest.ExtractEnergyByNumber 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 71: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 71: Pres. DC -268.49 3 8.52175 13.2804 (bar) 71: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyMixed 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 71: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 71: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 71: 13 Box-Z 14 Volume 15 Density 16 pV 71: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 71: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 71: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 71: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 71: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 71: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: [ OK ] EnergyTest.ExtractEnergyMixed (2 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (1 ms) 71: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 71: 71: Select the terms you want from the following list by 71: selecting either (part of) the name or the number or a combination. 71: End your selection with an empty line or a zero. 71: ------------------------------------------------------------------- 71: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 71: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 71: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 71: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 71: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 71: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 71: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 71: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 71: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 71: 37 1/Viscosity 38 T-System 39 Lamb-System 71: 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 71: 71: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 71: All statistics are over 3 points (frames) 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 71: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 71: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) 71: [----------] 5 tests from EnergyTest (15 ms total) 71: 71: [----------] 3 tests from ViscosityTest 71: [ RUN ] ViscosityTest.EinsteinViscosity 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosity (28 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityIntegral (17 ms) 71: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 71: Opened /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 71: 71: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 71: All statistics are over 5001 points 71: 71: Energy Average Err.Est. RMSD Tot-Drift 71: ------------------------------------------------------------------------------- 71: Pres-XX 20.2092 65 717.193 185.978 (bar) 71: Pres-XY -47.7351 39 372.522 207.456 (bar) 71: Pres-XZ 11.477 31 379.79 6.80818 (bar) 71: Pres-YX -47.7106 39 372.525 207.5 (bar) 71: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 71: Pres-YZ -41.3534 45 401.216 114.663 (bar) 71: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 71: Pres-ZY -41.3119 45 401.196 114.743 (bar) 71: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 71: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 71: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 71: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 71: 71: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 71: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (28 ms) 71: [----------] 3 tests from ViscosityTest (74 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 5 test suites ran. (123 ms total) 71: [ PASSED ] 12 tests. 71/104 Test #71: EnergyAnalysisUnitTests ................... Passed 0.15 sec test 72 Start 72: ToolUnitTests 72: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests 72: Test timeout computed to be: 1920 72: [==========] Running 70 tests from 8 test suites. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from DumpTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -1107434690 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] DumpTest.WorksWithTpr 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 72: inputrec: 72: integrator = md 72: tinit = 0 72: dt = 0.001 72: nsteps = 0 72: init-step = 0 72: simulation-part = 1 72: mts = false 72: mass-repartition-factor = 1 72: comm-mode = Linear 72: nstcomm = 100 72: bd-fric = 0 72: ld-seed = -1107434690 72: emtol = 10 72: emstep = 0.01 72: niter = 20 72: fcstep = 0 72: nstcgsteep = 1000 72: nbfgscorr = 10 72: rtpi = 0.05 72: nstxout = 0 72: nstvout = 0 72: nstfout = 0 72: nstlog = 1000 72: nstcalcenergy = 100 72: nstenergy = 1000 72: nstxout-compressed = 0 72: compressed-x-precision = 1000 72: cutoff-scheme = Verlet 72: nstlist = 10 72: pbc = xyz 72: periodic-molecules = false 72: verlet-buffer-tolerance = -1 72: verlet-buffer-pressure-tolerance = 0.5 72: rlist = 1.1 72: coulombtype = Cut-off 72: coulomb-modifier = Potential-shift 72: rcoulomb-switch = 0 72: rcoulomb = 1 72: epsilon-r = 1 72: epsilon-rf = inf 72: vdw-type = Cut-off 72: vdw-modifier = Potential-shift 72: rvdw-switch = 0 72: rvdw = 1 72: DispCorr = No 72: table-extension = 1 72: fourierspacing = 0.12 72: fourier-nx = 0 72: fourier-ny = 0 72: fourier-nz = 0 72: pme-order = 4 72: ewald-rtol = 1e-05 72: ewald-rtol-lj = 0.001 72: lj-pme-comb-rule = Geometric 72: ewald-geometry = 3d 72: epsilon-surface = 0 72: ensemble-temperature-setting = not available 72: tcoupl = No 72: nsttcouple = -1 72: nh-chain-length = 0 72: print-nose-hoover-chain-variables = false 72: pcoupl = No 72: refcoord-scaling = No 72: posres-com: not available 72: posres-comB: not available 72: QMMM = false 72: qm-opts: 72: ngQM = 0 72: constraint-algorithm = Lincs 72: continuation = false 72: Shake-SOR = false 72: shake-tol = 0.0001 72: lincs-order = 4 72: lincs-iter = 1 72: lincs-warnangle = 30 72: nwall = 0 72: wall-type = 9-3 72: wall-r-linpot = -1 72: wall-atomtype[0] = -1 72: wall-atomtype[1] = -1 72: wall-density[0] = 0 72: wall-density[1] = 0 72: wall-ewald-zfac = 3 72: pull = false 72: awh = false 72: rotation = false 72: interactiveMD = false 72: disre = No 72: disre-weighting = Conservative 72: disre-mixed = false 72: dr-fc = 1000 72: dr-tau = 0 72: nstdisreout = 100 72: orire-fc = 0 72: orire-tau = 0 72: nstorireout = 100 72: free-energy = no 72: cos-acceleration = 0 72: deform (3x3): 72: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: simulated-tempering = false 72: swapcoords = no 72: userint1 = 0 72: userint2 = 0 72: userint3 = 0 72: userint4 = 0 72: userreal1 = 0 72: userreal2 = 0 72: userreal3 = 0 72: userreal4 = 0 72: applied-forces: 72: electric-field: 72: x: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: y: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: z: 72: E0 = 0 72: omega = 0 72: t0 = 0 72: sigma = 0 72: density-guided-simulation: 72: active = false 72: group = protein 72: similarity-measure = inner-product 72: atom-spreading-weight = unity 72: force-constant = 1e+09 72: gaussian-transform-spreading-width = 0.2 72: gaussian-transform-spreading-range-in-multiples-of-width = 4 72: reference-density-filename = reference.mrc 72: nst = 1 72: normalize-densities = true 72: adaptive-force-scaling = false 72: adaptive-force-scaling-time-constant = 4 72: shift-vector = 72: transformation-matrix = 72: qmmm-cp2k: 72: active = false 72: qmgroup = System 72: qmmethod = PBE 72: qmfilenames = 72: qmcharge = 0 72: qmmultiplicity = 1 72: colvars: 72: active = false 72: configfile = 72: seed = -1 72: nnpot: 72: active = false 72: modelfile = model.pt 72: input-group = System 72: link-type = H 72: link-distance = 0.1 72: pair-cutoff = 0 72: embedding = mechanical 72: nnp-charge = 0 72: model-input1 = 72: model-input2 = 72: model-input3 = 72: model-input4 = 72: model-input5 = 72: model-input6 = 72: model-input7 = 72: model-input8 = 72: model-input9 = 72: fast-multipole-method: 72: fmm: 72: backend = inactive 72: exafmm-order = 6 72: exafmm-direct-range = 2 72: exafmm-direct-provider = GROMACS 72: exafmm-tree-type = uniform 72: exafmm-tree-depth = 0 72: exafmm-max-particles-per-cell = 0 72: fmsolvr-order = 8 72: fmsolvr-direct-range = 1 72: fmsolvr-direct-provider = FMM 72: fmsolvr-dipole-compensation = true 72: fmsolvr-tree-depth = 3 72: fmsolvr-sparse = false 72: grpopts: 72: nrdf: 465 72: ref-t: 0 72: tau-t: 0 72: annealing: No 72: annealing-npoints: 0 72: acc: 0 0 0 72: nfreeze: N N N 72: energygrp-flags[ 0]: 0 72: header: 72: bIr = present 72: bBox = present 72: bTop = present 72: bX = present 72: bV = present 72: bF = not present 72: natoms = 156 72: lambda = 0.000000e+00 72: buffer size = 57866 72: topology: 72: name="First 10 residues from 1AKI" 72: #atoms = 156 72: #molblock = 1 72: molblock (0): 72: moltype = 0 "Protein_chain_B" 72: #molecules = 1 72: #posres_xA = 0 72: #posres_xB = 0 72: bIntermolecularInteractions = false 72: ffparams: 72: atnr=10 72: ntypes=212 72: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 72: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 72: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 72: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 72: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 72: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 72: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 72: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 72: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 72: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 72: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 72: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 72: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 72: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 72: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 72: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 72: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 72: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 72: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 72: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 72: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 72: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 72: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 72: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 72: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 72: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 72: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 72: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 72: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 72: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 72: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 72: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 72: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 72: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 72: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 72: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 72: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 72: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 72: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 72: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 72: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 72: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 72: functype[56]=LJ_SR, c6= 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0.00000000e+00 72: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 72: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 72: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 72: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 72: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 72: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 72: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 72: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 72: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 72: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 72: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 72: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 72: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 72: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 72: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 72: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 72: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 72: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 72: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 72: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 72: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 72: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 72: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 72: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 72: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 72: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 72: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 72: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 72: reppow = 12 72: fudgeQQ = 0.5 72: cmap 72: moltype (0): 72: name="Protein_chain_B" 72: atoms: 72: atom (156): 72: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 72: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 72: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 72: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 72: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 72: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 72: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 72: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 72: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 72: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 72: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 72: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 72: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 72: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 72: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 72: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 72: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 72: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 72: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 72: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 72: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 72: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 72: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 72: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 72: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 72: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 72: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 72: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 72: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 72: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 72: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 72: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 72: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 72: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 72: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 72: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 72: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 72: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 72: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 72: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 72: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 72: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 72: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 72: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 72: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 72: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 72: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 72: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 72: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 72: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 72: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 72: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 72: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 72: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 72: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 72: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 72: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 72: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 72: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 72: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 72: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 72: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 72: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 72: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 72: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 72: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 72: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 72: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 72: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 72: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 72: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 72: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 72: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 72: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 72: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 72: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 72: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 72: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 72: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 72: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 72: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 72: atom (156): 72: atom[0]={name="N"} 72: atom[1]={name="H1"} 72: atom[2]={name="H2"} 72: atom[3]={name="H3"} 72: atom[4]={name="CA"} 72: atom[5]={name="HA"} 72: atom[6]={name="CB"} 72: atom[7]={name="HB1"} 72: atom[8]={name="HB2"} 72: atom[9]={name="CG"} 72: atom[10]={name="HG1"} 72: atom[11]={name="HG2"} 72: atom[12]={name="CD"} 72: atom[13]={name="HD1"} 72: atom[14]={name="HD2"} 72: atom[15]={name="CE"} 72: atom[16]={name="HE1"} 72: atom[17]={name="HE2"} 72: atom[18]={name="NZ"} 72: atom[19]={name="HZ1"} 72: atom[20]={name="HZ2"} 72: atom[21]={name="HZ3"} 72: atom[22]={name="C"} 72: atom[23]={name="O"} 72: atom[24]={name="N"} 72: atom[25]={name="H"} 72: atom[26]={name="CA"} 72: atom[27]={name="HA"} 72: atom[28]={name="CB"} 72: atom[29]={name="HB"} 72: atom[30]={name="CG1"} 72: atom[31]={name="HG11"} 72: atom[32]={name="HG12"} 72: atom[33]={name="HG13"} 72: atom[34]={name="CG2"} 72: atom[35]={name="HG21"} 72: atom[36]={name="HG22"} 72: atom[37]={name="HG23"} 72: atom[38]={name="C"} 72: atom[39]={name="O"} 72: atom[40]={name="N"} 72: atom[41]={name="H"} 72: atom[42]={name="CA"} 72: atom[43]={name="HA"} 72: atom[44]={name="CB"} 72: atom[45]={name="HB1"} 72: atom[46]={name="HB2"} 72: atom[47]={name="CG"} 72: atom[48]={name="CD1"} 72: atom[49]={name="HD1"} 72: atom[50]={name="CD2"} 72: atom[51]={name="HD2"} 72: atom[52]={name="CE1"} 72: atom[53]={name="HE1"} 72: atom[54]={name="CE2"} 72: atom[55]={name="HE2"} 72: atom[56]={name="CZ"} 72: atom[57]={name="HZ"} 72: atom[58]={name="C"} 72: atom[59]={name="O"} 72: atom[60]={name="N"} 72: atom[61]={name="H"} 72: atom[62]={name="CA"} 72: atom[63]={name="HA1"} 72: atom[64]={name="HA2"} 72: atom[65]={name="C"} 72: atom[66]={name="O"} 72: atom[67]={name="N"} 72: atom[68]={name="H"} 72: atom[69]={name="CA"} 72: atom[70]={name="HA"} 72: atom[71]={name="CB"} 72: atom[72]={name="HB1"} 72: atom[73]={name="HB2"} 72: atom[74]={name="CG"} 72: atom[75]={name="HG1"} 72: atom[76]={name="HG2"} 72: atom[77]={name="CD"} 72: atom[78]={name="HD1"} 72: atom[79]={name="HD2"} 72: atom[80]={name="NE"} 72: atom[81]={name="HE"} 72: atom[82]={name="CZ"} 72: atom[83]={name="NH1"} 72: atom[84]={name="HH11"} 72: atom[85]={name="HH12"} 72: atom[86]={name="NH2"} 72: atom[87]={name="HH21"} 72: atom[88]={name="HH22"} 72: atom[89]={name="C"} 72: atom[90]={name="O"} 72: atom[91]={name="N"} 72: atom[92]={name="H"} 72: atom[93]={name="CA"} 72: atom[94]={name="HA"} 72: atom[95]={name="CB"} 72: atom[96]={name="HB1"} 72: atom[97]={name="HB2"} 72: atom[98]={name="SG"} 72: atom[99]={name="HG"} 72: atom[100]={name="C"} 72: atom[101]={name="O"} 72: atom[102]={name="N"} 72: atom[103]={name="H"} 72: atom[104]={name="CA"} 72: atom[105]={name="HA"} 72: atom[106]={name="CB"} 72: atom[107]={name="HB1"} 72: atom[108]={name="HB2"} 72: atom[109]={name="CG"} 72: atom[110]={name="HG1"} 72: atom[111]={name="HG2"} 72: atom[112]={name="CD"} 72: atom[113]={name="OE1"} 72: atom[114]={name="OE2"} 72: atom[115]={name="C"} 72: atom[116]={name="O"} 72: atom[117]={name="N"} 72: atom[118]={name="H"} 72: atom[119]={name="CA"} 72: atom[120]={name="HA"} 72: atom[121]={name="CB"} 72: atom[122]={name="HB1"} 72: atom[123]={name="HB2"} 72: atom[124]={name="CG"} 72: atom[125]={name="HG"} 72: atom[126]={name="CD1"} 72: atom[127]={name="HD11"} 72: atom[128]={name="HD12"} 72: atom[129]={name="HD13"} 72: atom[130]={name="CD2"} 72: atom[131]={name="HD21"} 72: atom[132]={name="HD22"} 72: atom[133]={name="HD23"} 72: atom[134]={name="C"} 72: atom[135]={name="O"} 72: atom[136]={name="N"} 72: atom[137]={name="H"} 72: atom[138]={name="CA"} 72: atom[139]={name="HA"} 72: atom[140]={name="CB"} 72: atom[141]={name="HB1"} 72: atom[142]={name="HB2"} 72: atom[143]={name="HB3"} 72: atom[144]={name="C"} 72: atom[145]={name="O"} 72: atom[146]={name="N"} 72: atom[147]={name="H"} 72: atom[148]={name="CA"} 72: atom[149]={name="HA"} 72: atom[150]={name="CB"} 72: atom[151]={name="HB1"} 72: atom[152]={name="HB2"} 72: atom[153]={name="HB3"} 72: atom[154]={name="C"} 72: atom[155]={name="O"} 72: type (156): 72: type[0]={name="opls_287",nameB="opls_287"} 72: type[1]={name="opls_290",nameB="opls_290"} 72: type[2]={name="opls_290",nameB="opls_290"} 72: type[3]={name="opls_290",nameB="opls_290"} 72: type[4]={name="opls_293B",nameB="opls_293B"} 72: type[5]={name="opls_140",nameB="opls_140"} 72: type[6]={name="opls_136",nameB="opls_136"} 72: type[7]={name="opls_140",nameB="opls_140"} 72: type[8]={name="opls_140",nameB="opls_140"} 72: type[9]={name="opls_136",nameB="opls_136"} 72: type[10]={name="opls_140",nameB="opls_140"} 72: type[11]={name="opls_140",nameB="opls_140"} 72: type[12]={name="opls_136",nameB="opls_136"} 72: type[13]={name="opls_140",nameB="opls_140"} 72: type[14]={name="opls_140",nameB="opls_140"} 72: type[15]={name="opls_292",nameB="opls_292"} 72: type[16]={name="opls_140",nameB="opls_140"} 72: type[17]={name="opls_140",nameB="opls_140"} 72: type[18]={name="opls_287",nameB="opls_287"} 72: type[19]={name="opls_290",nameB="opls_290"} 72: type[20]={name="opls_290",nameB="opls_290"} 72: type[21]={name="opls_290",nameB="opls_290"} 72: type[22]={name="opls_235",nameB="opls_235"} 72: type[23]={name="opls_236",nameB="opls_236"} 72: type[24]={name="opls_238",nameB="opls_238"} 72: type[25]={name="opls_241",nameB="opls_241"} 72: type[26]={name="opls_224B",nameB="opls_224B"} 72: type[27]={name="opls_140",nameB="opls_140"} 72: type[28]={name="opls_137",nameB="opls_137"} 72: type[29]={name="opls_140",nameB="opls_140"} 72: type[30]={name="opls_135",nameB="opls_135"} 72: type[31]={name="opls_140",nameB="opls_140"} 72: type[32]={name="opls_140",nameB="opls_140"} 72: type[33]={name="opls_140",nameB="opls_140"} 72: type[34]={name="opls_135",nameB="opls_135"} 72: type[35]={name="opls_140",nameB="opls_140"} 72: type[36]={name="opls_140",nameB="opls_140"} 72: type[37]={name="opls_140",nameB="opls_140"} 72: type[38]={name="opls_235",nameB="opls_235"} 72: type[39]={name="opls_236",nameB="opls_236"} 72: type[40]={name="opls_238",nameB="opls_238"} 72: type[41]={name="opls_241",nameB="opls_241"} 72: type[42]={name="opls_224B",nameB="opls_224B"} 72: type[43]={name="opls_140",nameB="opls_140"} 72: type[44]={name="opls_149",nameB="opls_149"} 72: type[45]={name="opls_140",nameB="opls_140"} 72: type[46]={name="opls_140",nameB="opls_140"} 72: type[47]={name="opls_145",nameB="opls_145"} 72: type[48]={name="opls_145",nameB="opls_145"} 72: type[49]={name="opls_146",nameB="opls_146"} 72: type[50]={name="opls_145",nameB="opls_145"} 72: type[51]={name="opls_146",nameB="opls_146"} 72: type[52]={name="opls_145",nameB="opls_145"} 72: type[53]={name="opls_146",nameB="opls_146"} 72: type[54]={name="opls_145",nameB="opls_145"} 72: type[55]={name="opls_146",nameB="opls_146"} 72: type[56]={name="opls_145",nameB="opls_145"} 72: type[57]={name="opls_146",nameB="opls_146"} 72: type[58]={name="opls_235",nameB="opls_235"} 72: type[59]={name="opls_236",nameB="opls_236"} 72: type[60]={name="opls_238",nameB="opls_238"} 72: type[61]={name="opls_241",nameB="opls_241"} 72: type[62]={name="opls_223B",nameB="opls_223B"} 72: type[63]={name="opls_140",nameB="opls_140"} 72: type[64]={name="opls_140",nameB="opls_140"} 72: type[65]={name="opls_235",nameB="opls_235"} 72: type[66]={name="opls_236",nameB="opls_236"} 72: type[67]={name="opls_238",nameB="opls_238"} 72: type[68]={name="opls_241",nameB="opls_241"} 72: type[69]={name="opls_224B",nameB="opls_224B"} 72: type[70]={name="opls_140",nameB="opls_140"} 72: type[71]={name="opls_136",nameB="opls_136"} 72: type[72]={name="opls_140",nameB="opls_140"} 72: type[73]={name="opls_140",nameB="opls_140"} 72: type[74]={name="opls_308",nameB="opls_308"} 72: type[75]={name="opls_140",nameB="opls_140"} 72: type[76]={name="opls_140",nameB="opls_140"} 72: type[77]={name="opls_307",nameB="opls_307"} 72: type[78]={name="opls_140",nameB="opls_140"} 72: type[79]={name="opls_140",nameB="opls_140"} 72: type[80]={name="opls_303",nameB="opls_303"} 72: type[81]={name="opls_304",nameB="opls_304"} 72: type[82]={name="opls_302",nameB="opls_302"} 72: type[83]={name="opls_300",nameB="opls_300"} 72: type[84]={name="opls_301",nameB="opls_301"} 72: type[85]={name="opls_301",nameB="opls_301"} 72: type[86]={name="opls_300",nameB="opls_300"} 72: type[87]={name="opls_301",nameB="opls_301"} 72: type[88]={name="opls_301",nameB="opls_301"} 72: type[89]={name="opls_235",nameB="opls_235"} 72: type[90]={name="opls_236",nameB="opls_236"} 72: type[91]={name="opls_238",nameB="opls_238"} 72: type[92]={name="opls_241",nameB="opls_241"} 72: type[93]={name="opls_224B",nameB="opls_224B"} 72: type[94]={name="opls_140",nameB="opls_140"} 72: type[95]={name="opls_206",nameB="opls_206"} 72: type[96]={name="opls_140",nameB="opls_140"} 72: type[97]={name="opls_140",nameB="opls_140"} 72: type[98]={name="opls_200",nameB="opls_200"} 72: type[99]={name="opls_204",nameB="opls_204"} 72: type[100]={name="opls_235",nameB="opls_235"} 72: type[101]={name="opls_236",nameB="opls_236"} 72: type[102]={name="opls_238",nameB="opls_238"} 72: type[103]={name="opls_241",nameB="opls_241"} 72: type[104]={name="opls_224B",nameB="opls_224B"} 72: type[105]={name="opls_140",nameB="opls_140"} 72: type[106]={name="opls_136",nameB="opls_136"} 72: type[107]={name="opls_140",nameB="opls_140"} 72: type[108]={name="opls_140",nameB="opls_140"} 72: type[109]={name="opls_274",nameB="opls_274"} 72: type[110]={name="opls_140",nameB="opls_140"} 72: type[111]={name="opls_140",nameB="opls_140"} 72: type[112]={name="opls_271",nameB="opls_271"} 72: type[113]={name="opls_272",nameB="opls_272"} 72: type[114]={name="opls_272",nameB="opls_272"} 72: type[115]={name="opls_235",nameB="opls_235"} 72: type[116]={name="opls_236",nameB="opls_236"} 72: type[117]={name="opls_238",nameB="opls_238"} 72: type[118]={name="opls_241",nameB="opls_241"} 72: type[119]={name="opls_224B",nameB="opls_224B"} 72: type[120]={name="opls_140",nameB="opls_140"} 72: type[121]={name="opls_136",nameB="opls_136"} 72: type[122]={name="opls_140",nameB="opls_140"} 72: type[123]={name="opls_140",nameB="opls_140"} 72: type[124]={name="opls_137",nameB="opls_137"} 72: type[125]={name="opls_140",nameB="opls_140"} 72: type[126]={name="opls_135",nameB="opls_135"} 72: type[127]={name="opls_140",nameB="opls_140"} 72: type[128]={name="opls_140",nameB="opls_140"} 72: type[129]={name="opls_140",nameB="opls_140"} 72: type[130]={name="opls_135",nameB="opls_135"} 72: type[131]={name="opls_140",nameB="opls_140"} 72: type[132]={name="opls_140",nameB="opls_140"} 72: type[133]={name="opls_140",nameB="opls_140"} 72: type[134]={name="opls_235",nameB="opls_235"} 72: type[135]={name="opls_236",nameB="opls_236"} 72: type[136]={name="opls_238",nameB="opls_238"} 72: type[137]={name="opls_241",nameB="opls_241"} 72: type[138]={name="opls_224B",nameB="opls_224B"} 72: type[139]={name="opls_140",nameB="opls_140"} 72: type[140]={name="opls_135",nameB="opls_135"} 72: type[141]={name="opls_140",nameB="opls_140"} 72: type[142]={name="opls_140",nameB="opls_140"} 72: type[143]={name="opls_140",nameB="opls_140"} 72: type[144]={name="opls_235",nameB="opls_235"} 72: type[145]={name="opls_236",nameB="opls_236"} 72: type[146]={name="opls_238",nameB="opls_238"} 72: type[147]={name="opls_241",nameB="opls_241"} 72: type[148]={name="opls_224B",nameB="opls_224B"} 72: type[149]={name="opls_140",nameB="opls_140"} 72: type[150]={name="opls_135",nameB="opls_135"} 72: type[151]={name="opls_140",nameB="opls_140"} 72: type[152]={name="opls_140",nameB="opls_140"} 72: type[153]={name="opls_140",nameB="opls_140"} 72: type[154]={name="opls_235",nameB="opls_235"} 72: type[155]={name="opls_236",nameB="opls_236"} 72: residue (10): 72: residue[0]={name="LYS", nr=1, ic=' '} 72: residue[1]={name="VAL", nr=2, ic=' '} 72: residue[2]={name="PHE", nr=3, ic=' '} 72: residue[3]={name="GLY", nr=4, ic=' '} 72: residue[4]={name="ARG", nr=5, ic=' '} 72: residue[5]={name="CYS", nr=6, ic=' '} 72: residue[6]={name="GLU", nr=7, ic=' '} 72: residue[7]={name="LEU", nr=8, ic=' '} 72: residue[8]={name="ALA", nr=9, ic=' '} 72: residue[9]={name="ALA", nr=10, ic=' '} 72: excls: 72: numLists=156 72: numElements=1828 72: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 72: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 72: 23, 24, 25, 26} 72: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 72: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 72: 14, 15, 22, 23, 24} 72: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 72: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 72: 16, 17, 18, 22} 72: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 72: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 72: 17, 18, 19, 20, 21} 72: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 72: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 72: 20, 21} 72: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 72: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 72: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 72: 26, 27, 28, 38} 72: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 72: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 72: 30, 34, 38, 39, 40} 72: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 72: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 72: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 72: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40} 72: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 72: 34, 35, 36, 37, 38, 39, 40} 72: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 72: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 72: 36, 37, 38} 72: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 72: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 72: 40, 41, 42, 43, 44, 58} 72: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 72: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 72: 45, 46, 47, 58, 59, 60} 72: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 72: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 72: 48, 50, 58, 59, 60, 61, 62} 72: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60} 72: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 72: 50, 51, 52, 54, 58, 59, 60} 72: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 72: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 72: 52, 53, 54, 55, 56, 58} 72: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 72: 54, 56, 57} 72: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 72: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 72: 55, 56, 57} 72: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 72: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 72: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 72: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 72: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 72: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 72: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 72: 60, 61, 62, 63, 64, 65} 72: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 72: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 72: 65, 66, 67} 72: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 72: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 72: 68, 69} 72: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 72: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 72: 70, 71, 89} 72: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 72: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72: 72, 73, 74, 89, 90, 91} 72: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 72: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 72: 75, 76, 77, 89, 90, 91, 92, 93} 72: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91} 72: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 72: 77, 78, 79, 80, 89, 90, 91} 72: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 72: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 72: 79, 80, 81, 82, 89} 72: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 72: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 72: 81, 82, 83, 86} 72: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 72: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 72: 84, 85, 86, 87, 88} 72: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 72: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 72: 87, 88} 72: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[84][num=6]={80, 82, 83, 84, 85, 86} 72: excls[85][num=6]={80, 82, 83, 84, 85, 86} 72: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 72: excls[87][num=6]={80, 82, 83, 86, 87, 88} 72: excls[88][num=6]={80, 82, 83, 86, 87, 88} 72: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 72: 91, 92, 93, 94, 95, 100} 72: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 72: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 72: 96, 97, 98, 100, 101, 102} 72: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 72: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 72: 99, 100, 101, 102, 103, 104} 72: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102} 72: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 72: 101, 102} 72: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 72: excls[99][num=6]={93, 95, 96, 97, 98, 99} 72: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 72: 102, 103, 104, 105, 106, 115} 72: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 72: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 72: 106, 107, 108, 109, 115, 116, 117} 72: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 72: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 72: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 72: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117} 72: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 110, 111, 112, 113, 114, 115, 116, 117} 72: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 115} 72: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 72: 112, 113, 114, 115} 72: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 72: 114} 72: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 72: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 72: 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 72: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 72: 120, 121, 122, 123, 124, 134, 135, 136} 72: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 72: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 72: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 72: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136} 72: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 72: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 130, 134} 72: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 72: 127, 128, 129, 130, 131, 132, 133, 134} 72: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 72: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 72: 129, 130, 131, 132, 133} 72: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 72: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 72: 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 72: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 72: 139, 140, 141, 142, 143, 144, 145, 146} 72: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 72: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 72: 142, 143, 144, 145, 146, 147, 148} 72: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146} 72: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 72: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 72: 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 72: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 72: 149, 150, 151, 152, 153, 154, 155} 72: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 72: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 72: 152, 153, 154, 155} 72: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 72: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 72: 154, 155} 72: excls[155][num=6]={146, 148, 149, 150, 154, 155} 72: Bond: 72: nr: 468 72: iatoms: 72: 0 type=100 (BONDS) 0 1 72: 1 type=100 (BONDS) 0 2 72: 2 type=100 (BONDS) 0 3 72: 3 type=101 (BONDS) 0 4 72: 4 type=102 (BONDS) 4 5 72: 5 type=103 (BONDS) 4 6 72: 6 type=104 (BONDS) 4 22 72: 7 type=102 (BONDS) 6 7 72: 8 type=102 (BONDS) 6 8 72: 9 type=103 (BONDS) 6 9 72: 10 type=102 (BONDS) 9 10 72: 11 type=102 (BONDS) 9 11 72: 12 type=103 (BONDS) 9 12 72: 13 type=102 (BONDS) 12 13 72: 14 type=102 (BONDS) 12 14 72: 15 type=103 (BONDS) 12 15 72: 16 type=102 (BONDS) 15 16 72: 17 type=102 (BONDS) 15 17 72: 18 type=101 (BONDS) 15 18 72: 19 type=100 (BONDS) 18 19 72: 20 type=100 (BONDS) 18 20 72: 21 type=100 (BONDS) 18 21 72: 22 type=105 (BONDS) 22 23 72: 23 type=106 (BONDS) 22 24 72: 24 type=100 (BONDS) 24 25 72: 25 type=107 (BONDS) 24 26 72: 26 type=102 (BONDS) 26 27 72: 27 type=103 (BONDS) 26 28 72: 28 type=104 (BONDS) 26 38 72: 29 type=102 (BONDS) 28 29 72: 30 type=103 (BONDS) 28 30 72: 31 type=103 (BONDS) 28 34 72: 32 type=102 (BONDS) 30 31 72: 33 type=102 (BONDS) 30 32 72: 34 type=102 (BONDS) 30 33 72: 35 type=102 (BONDS) 34 35 72: 36 type=102 (BONDS) 34 36 72: 37 type=102 (BONDS) 34 37 72: 38 type=105 (BONDS) 38 39 72: 39 type=106 (BONDS) 38 40 72: 40 type=100 (BONDS) 40 41 72: 41 type=107 (BONDS) 40 42 72: 42 type=102 (BONDS) 42 43 72: 43 type=103 (BONDS) 42 44 72: 44 type=104 (BONDS) 42 58 72: 45 type=102 (BONDS) 44 45 72: 46 type=102 (BONDS) 44 46 72: 47 type=108 (BONDS) 44 47 72: 48 type=109 (BONDS) 47 48 72: 49 type=109 (BONDS) 47 50 72: 50 type=110 (BONDS) 48 49 72: 51 type=109 (BONDS) 48 52 72: 52 type=110 (BONDS) 50 51 72: 53 type=109 (BONDS) 50 54 72: 54 type=110 (BONDS) 52 53 72: 55 type=109 (BONDS) 52 56 72: 56 type=110 (BONDS) 54 55 72: 57 type=109 (BONDS) 54 56 72: 58 type=110 (BONDS) 56 57 72: 59 type=105 (BONDS) 58 59 72: 60 type=106 (BONDS) 58 60 72: 61 type=100 (BONDS) 60 61 72: 62 type=107 (BONDS) 60 62 72: 63 type=102 (BONDS) 62 63 72: 64 type=102 (BONDS) 62 64 72: 65 type=104 (BONDS) 62 65 72: 66 type=105 (BONDS) 65 66 72: 67 type=106 (BONDS) 65 67 72: 68 type=100 (BONDS) 67 68 72: 69 type=107 (BONDS) 67 69 72: 70 type=102 (BONDS) 69 70 72: 71 type=103 (BONDS) 69 71 72: 72 type=104 (BONDS) 69 89 72: 73 type=102 (BONDS) 71 72 72: 74 type=102 (BONDS) 71 73 72: 75 type=103 (BONDS) 71 74 72: 76 type=102 (BONDS) 74 75 72: 77 type=102 (BONDS) 74 76 72: 78 type=103 (BONDS) 74 77 72: 79 type=102 (BONDS) 77 78 72: 80 type=102 (BONDS) 77 79 72: 81 type=111 (BONDS) 77 80 72: 82 type=100 (BONDS) 80 81 72: 83 type=112 (BONDS) 80 82 72: 84 type=112 (BONDS) 82 83 72: 85 type=112 (BONDS) 82 86 72: 86 type=100 (BONDS) 83 84 72: 87 type=100 (BONDS) 83 85 72: 88 type=100 (BONDS) 86 87 72: 89 type=100 (BONDS) 86 88 72: 90 type=105 (BONDS) 89 90 72: 91 type=106 (BONDS) 89 91 72: 92 type=100 (BONDS) 91 92 72: 93 type=107 (BONDS) 91 93 72: 94 type=102 (BONDS) 93 94 72: 95 type=103 (BONDS) 93 95 72: 96 type=104 (BONDS) 93 100 72: 97 type=102 (BONDS) 95 96 72: 98 type=102 (BONDS) 95 97 72: 99 type=113 (BONDS) 95 98 72: 100 type=114 (BONDS) 98 99 72: 101 type=105 (BONDS) 100 101 72: 102 type=106 (BONDS) 100 102 72: 103 type=100 (BONDS) 102 103 72: 104 type=107 (BONDS) 102 104 72: 105 type=102 (BONDS) 104 105 72: 106 type=103 (BONDS) 104 106 72: 107 type=104 (BONDS) 104 115 72: 108 type=102 (BONDS) 106 107 72: 109 type=102 (BONDS) 106 108 72: 110 type=103 (BONDS) 106 109 72: 111 type=102 (BONDS) 109 110 72: 112 type=102 (BONDS) 109 111 72: 113 type=104 (BONDS) 109 112 72: 114 type=115 (BONDS) 112 113 72: 115 type=115 (BONDS) 112 114 72: 116 type=105 (BONDS) 115 116 72: 117 type=106 (BONDS) 115 117 72: 118 type=100 (BONDS) 117 118 72: 119 type=107 (BONDS) 117 119 72: 120 type=102 (BONDS) 119 120 72: 121 type=103 (BONDS) 119 121 72: 122 type=104 (BONDS) 119 134 72: 123 type=102 (BONDS) 121 122 72: 124 type=102 (BONDS) 121 123 72: 125 type=103 (BONDS) 121 124 72: 126 type=102 (BONDS) 124 125 72: 127 type=103 (BONDS) 124 126 72: 128 type=103 (BONDS) 124 130 72: 129 type=102 (BONDS) 126 127 72: 130 type=102 (BONDS) 126 128 72: 131 type=102 (BONDS) 126 129 72: 132 type=102 (BONDS) 130 131 72: 133 type=102 (BONDS) 130 132 72: 134 type=102 (BONDS) 130 133 72: 135 type=105 (BONDS) 134 135 72: 136 type=106 (BONDS) 134 136 72: 137 type=100 (BONDS) 136 137 72: 138 type=107 (BONDS) 136 138 72: 139 type=102 (BONDS) 138 139 72: 140 type=103 (BONDS) 138 140 72: 141 type=104 (BONDS) 138 144 72: 142 type=102 (BONDS) 140 141 72: 143 type=102 (BONDS) 140 142 72: 144 type=102 (BONDS) 140 143 72: 145 type=105 (BONDS) 144 145 72: 146 type=106 (BONDS) 144 146 72: 147 type=100 (BONDS) 146 147 72: 148 type=107 (BONDS) 146 148 72: 149 type=102 (BONDS) 148 149 72: 150 type=103 (BONDS) 148 150 72: 151 type=104 (BONDS) 148 154 72: 152 type=102 (BONDS) 150 151 72: 153 type=102 (BONDS) 150 152 72: 154 type=102 (BONDS) 150 153 72: 155 type=105 (BONDS) 154 155 72: G96Bond: 72: nr: 0 72: Morse: 72: nr: 0 72: Cubic Bonds: 72: nr: 0 72: Connect Bonds: 72: nr: 0 72: Harmonic Pot.: 72: nr: 0 72: FENE Bonds: 72: nr: 0 72: Tab. Bonds: 72: nr: 0 72: Tab. Bonds NC: 72: nr: 0 72: Restraint Pot.: 72: nr: 0 72: Angle: 72: nr: 1124 72: iatoms: 72: 0 type=116 (ANGLES) 1 0 2 72: 1 type=116 (ANGLES) 1 0 3 72: 2 type=116 (ANGLES) 1 0 4 72: 3 type=116 (ANGLES) 2 0 3 72: 4 type=116 (ANGLES) 2 0 4 72: 5 type=116 (ANGLES) 3 0 4 72: 6 type=116 (ANGLES) 0 4 5 72: 7 type=117 (ANGLES) 0 4 6 72: 8 type=117 (ANGLES) 0 4 22 72: 9 type=118 (ANGLES) 5 4 6 72: 10 type=116 (ANGLES) 5 4 22 72: 11 type=119 (ANGLES) 6 4 22 72: 12 type=118 (ANGLES) 4 6 7 72: 13 type=118 (ANGLES) 4 6 8 72: 14 type=120 (ANGLES) 4 6 9 72: 15 type=121 (ANGLES) 7 6 8 72: 16 type=118 (ANGLES) 7 6 9 72: 17 type=118 (ANGLES) 8 6 9 72: 18 type=118 (ANGLES) 6 9 10 72: 19 type=118 (ANGLES) 6 9 11 72: 20 type=120 (ANGLES) 6 9 12 72: 21 type=121 (ANGLES) 10 9 11 72: 22 type=118 (ANGLES) 10 9 12 72: 23 type=118 (ANGLES) 11 9 12 72: 24 type=118 (ANGLES) 9 12 13 72: 25 type=118 (ANGLES) 9 12 14 72: 26 type=120 (ANGLES) 9 12 15 72: 27 type=121 (ANGLES) 13 12 14 72: 28 type=118 (ANGLES) 13 12 15 72: 29 type=118 (ANGLES) 14 12 15 72: 30 type=118 (ANGLES) 12 15 16 72: 31 type=118 (ANGLES) 12 15 17 72: 32 type=117 (ANGLES) 12 15 18 72: 33 type=121 (ANGLES) 16 15 17 72: 34 type=116 (ANGLES) 16 15 18 72: 35 type=116 (ANGLES) 17 15 18 72: 36 type=116 (ANGLES) 15 18 19 72: 37 type=116 (ANGLES) 15 18 20 72: 38 type=116 (ANGLES) 15 18 21 72: 39 type=116 (ANGLES) 19 18 20 72: 40 type=116 (ANGLES) 19 18 21 72: 41 type=116 (ANGLES) 20 18 21 72: 42 type=122 (ANGLES) 4 22 23 72: 43 type=123 (ANGLES) 4 22 24 72: 44 type=124 (ANGLES) 23 22 24 72: 45 type=125 (ANGLES) 22 24 25 72: 46 type=126 (ANGLES) 22 24 26 72: 47 type=127 (ANGLES) 25 24 26 72: 48 type=116 (ANGLES) 24 26 27 72: 49 type=128 (ANGLES) 24 26 28 72: 50 type=129 (ANGLES) 24 26 38 72: 51 type=118 (ANGLES) 27 26 28 72: 52 type=116 (ANGLES) 27 26 38 72: 53 type=119 (ANGLES) 28 26 38 72: 54 type=118 (ANGLES) 26 28 29 72: 55 type=120 (ANGLES) 26 28 30 72: 56 type=120 (ANGLES) 26 28 34 72: 57 type=118 (ANGLES) 29 28 30 72: 58 type=118 (ANGLES) 29 28 34 72: 59 type=120 (ANGLES) 30 28 34 72: 60 type=118 (ANGLES) 28 30 31 72: 61 type=118 (ANGLES) 28 30 32 72: 62 type=118 (ANGLES) 28 30 33 72: 63 type=121 (ANGLES) 31 30 32 72: 64 type=121 (ANGLES) 31 30 33 72: 65 type=121 (ANGLES) 32 30 33 72: 66 type=118 (ANGLES) 28 34 35 72: 67 type=118 (ANGLES) 28 34 36 72: 68 type=118 (ANGLES) 28 34 37 72: 69 type=121 (ANGLES) 35 34 36 72: 70 type=121 (ANGLES) 35 34 37 72: 71 type=121 (ANGLES) 36 34 37 72: 72 type=122 (ANGLES) 26 38 39 72: 73 type=123 (ANGLES) 26 38 40 72: 74 type=124 (ANGLES) 39 38 40 72: 75 type=125 (ANGLES) 38 40 41 72: 76 type=126 (ANGLES) 38 40 42 72: 77 type=127 (ANGLES) 41 40 42 72: 78 type=116 (ANGLES) 40 42 43 72: 79 type=128 (ANGLES) 40 42 44 72: 80 type=129 (ANGLES) 40 42 58 72: 81 type=118 (ANGLES) 43 42 44 72: 82 type=116 (ANGLES) 43 42 58 72: 83 type=119 (ANGLES) 44 42 58 72: 84 type=118 (ANGLES) 42 44 45 72: 85 type=118 (ANGLES) 42 44 46 72: 86 type=130 (ANGLES) 42 44 47 72: 87 type=121 (ANGLES) 45 44 46 72: 88 type=116 (ANGLES) 45 44 47 72: 89 type=116 (ANGLES) 46 44 47 72: 90 type=131 (ANGLES) 44 47 48 72: 91 type=131 (ANGLES) 44 47 50 72: 92 type=132 (ANGLES) 48 47 50 72: 93 type=133 (ANGLES) 47 48 49 72: 94 type=132 (ANGLES) 47 48 52 72: 95 type=133 (ANGLES) 49 48 52 72: 96 type=133 (ANGLES) 47 50 51 72: 97 type=132 (ANGLES) 47 50 54 72: 98 type=133 (ANGLES) 51 50 54 72: 99 type=133 (ANGLES) 48 52 53 72: 100 type=132 (ANGLES) 48 52 56 72: 101 type=133 (ANGLES) 53 52 56 72: 102 type=133 (ANGLES) 50 54 55 72: 103 type=132 (ANGLES) 50 54 56 72: 104 type=133 (ANGLES) 55 54 56 72: 105 type=132 (ANGLES) 52 56 54 72: 106 type=133 (ANGLES) 52 56 57 72: 107 type=133 (ANGLES) 54 56 57 72: 108 type=122 (ANGLES) 42 58 59 72: 109 type=123 (ANGLES) 42 58 60 72: 110 type=124 (ANGLES) 59 58 60 72: 111 type=125 (ANGLES) 58 60 61 72: 112 type=126 (ANGLES) 58 60 62 72: 113 type=127 (ANGLES) 61 60 62 72: 114 type=116 (ANGLES) 60 62 63 72: 115 type=116 (ANGLES) 60 62 64 72: 116 type=129 (ANGLES) 60 62 65 72: 117 type=121 (ANGLES) 63 62 64 72: 118 type=116 (ANGLES) 63 62 65 72: 119 type=116 (ANGLES) 64 62 65 72: 120 type=122 (ANGLES) 62 65 66 72: 121 type=123 (ANGLES) 62 65 67 72: 122 type=124 (ANGLES) 66 65 67 72: 123 type=125 (ANGLES) 65 67 68 72: 124 type=126 (ANGLES) 65 67 69 72: 125 type=127 (ANGLES) 68 67 69 72: 126 type=116 (ANGLES) 67 69 70 72: 127 type=128 (ANGLES) 67 69 71 72: 128 type=129 (ANGLES) 67 69 89 72: 129 type=118 (ANGLES) 70 69 71 72: 130 type=116 (ANGLES) 70 69 89 72: 131 type=119 (ANGLES) 71 69 89 72: 132 type=118 (ANGLES) 69 71 72 72: 133 type=118 (ANGLES) 69 71 73 72: 134 type=120 (ANGLES) 69 71 74 72: 135 type=121 (ANGLES) 72 71 73 72: 136 type=118 (ANGLES) 72 71 74 72: 137 type=118 (ANGLES) 73 71 74 72: 138 type=118 (ANGLES) 71 74 75 72: 139 type=118 (ANGLES) 71 74 76 72: 140 type=120 (ANGLES) 71 74 77 72: 141 type=121 (ANGLES) 75 74 76 72: 142 type=118 (ANGLES) 75 74 77 72: 143 type=118 (ANGLES) 76 74 77 72: 144 type=118 (ANGLES) 74 77 78 72: 145 type=118 (ANGLES) 74 77 79 72: 146 type=117 (ANGLES) 74 77 80 72: 147 type=121 (ANGLES) 78 77 79 72: 148 type=116 (ANGLES) 78 77 80 72: 149 type=116 (ANGLES) 79 77 80 72: 150 type=134 (ANGLES) 77 80 81 72: 151 type=135 (ANGLES) 77 80 82 72: 152 type=133 (ANGLES) 81 80 82 72: 153 type=131 (ANGLES) 80 82 83 72: 154 type=131 (ANGLES) 80 82 86 72: 155 type=131 (ANGLES) 83 82 86 72: 156 type=133 (ANGLES) 82 83 84 72: 157 type=133 (ANGLES) 82 83 85 72: 158 type=133 (ANGLES) 84 83 85 72: 159 type=133 (ANGLES) 82 86 87 72: 160 type=133 (ANGLES) 82 86 88 72: 161 type=133 (ANGLES) 87 86 88 72: 162 type=122 (ANGLES) 69 89 90 72: 163 type=123 (ANGLES) 69 89 91 72: 164 type=124 (ANGLES) 90 89 91 72: 165 type=125 (ANGLES) 89 91 92 72: 166 type=126 (ANGLES) 89 91 93 72: 167 type=127 (ANGLES) 92 91 93 72: 168 type=116 (ANGLES) 91 93 94 72: 169 type=128 (ANGLES) 91 93 95 72: 170 type=129 (ANGLES) 91 93 100 72: 171 type=118 (ANGLES) 94 93 95 72: 172 type=116 (ANGLES) 94 93 100 72: 173 type=119 (ANGLES) 95 93 100 72: 174 type=118 (ANGLES) 93 95 96 72: 175 type=118 (ANGLES) 93 95 97 72: 176 type=136 (ANGLES) 93 95 98 72: 177 type=121 (ANGLES) 96 95 97 72: 178 type=116 (ANGLES) 96 95 98 72: 179 type=116 (ANGLES) 97 95 98 72: 180 type=137 (ANGLES) 95 98 99 72: 181 type=122 (ANGLES) 93 100 101 72: 182 type=123 (ANGLES) 93 100 102 72: 183 type=124 (ANGLES) 101 100 102 72: 184 type=125 (ANGLES) 100 102 103 72: 185 type=126 (ANGLES) 100 102 104 72: 186 type=127 (ANGLES) 103 102 104 72: 187 type=116 (ANGLES) 102 104 105 72: 188 type=128 (ANGLES) 102 104 106 72: 189 type=129 (ANGLES) 102 104 115 72: 190 type=118 (ANGLES) 105 104 106 72: 191 type=116 (ANGLES) 105 104 115 72: 192 type=119 (ANGLES) 106 104 115 72: 193 type=118 (ANGLES) 104 106 107 72: 194 type=118 (ANGLES) 104 106 108 72: 195 type=120 (ANGLES) 104 106 109 72: 196 type=121 (ANGLES) 107 106 108 72: 197 type=118 (ANGLES) 107 106 109 72: 198 type=118 (ANGLES) 108 106 109 72: 199 type=118 (ANGLES) 106 109 110 72: 200 type=118 (ANGLES) 106 109 111 72: 201 type=119 (ANGLES) 106 109 112 72: 202 type=121 (ANGLES) 110 109 111 72: 203 type=116 (ANGLES) 110 109 112 72: 204 type=116 (ANGLES) 111 109 112 72: 205 type=138 (ANGLES) 109 112 113 72: 206 type=138 (ANGLES) 109 112 114 72: 207 type=139 (ANGLES) 113 112 114 72: 208 type=122 (ANGLES) 104 115 116 72: 209 type=123 (ANGLES) 104 115 117 72: 210 type=124 (ANGLES) 116 115 117 72: 211 type=125 (ANGLES) 115 117 118 72: 212 type=126 (ANGLES) 115 117 119 72: 213 type=127 (ANGLES) 118 117 119 72: 214 type=116 (ANGLES) 117 119 120 72: 215 type=128 (ANGLES) 117 119 121 72: 216 type=129 (ANGLES) 117 119 134 72: 217 type=118 (ANGLES) 120 119 121 72: 218 type=116 (ANGLES) 120 119 134 72: 219 type=119 (ANGLES) 121 119 134 72: 220 type=118 (ANGLES) 119 121 122 72: 221 type=118 (ANGLES) 119 121 123 72: 222 type=120 (ANGLES) 119 121 124 72: 223 type=121 (ANGLES) 122 121 123 72: 224 type=118 (ANGLES) 122 121 124 72: 225 type=118 (ANGLES) 123 121 124 72: 226 type=118 (ANGLES) 121 124 125 72: 227 type=120 (ANGLES) 121 124 126 72: 228 type=120 (ANGLES) 121 124 130 72: 229 type=118 (ANGLES) 125 124 126 72: 230 type=118 (ANGLES) 125 124 130 72: 231 type=120 (ANGLES) 126 124 130 72: 232 type=118 (ANGLES) 124 126 127 72: 233 type=118 (ANGLES) 124 126 128 72: 234 type=118 (ANGLES) 124 126 129 72: 235 type=121 (ANGLES) 127 126 128 72: 236 type=121 (ANGLES) 127 126 129 72: 237 type=121 (ANGLES) 128 126 129 72: 238 type=118 (ANGLES) 124 130 131 72: 239 type=118 (ANGLES) 124 130 132 72: 240 type=118 (ANGLES) 124 130 133 72: 241 type=121 (ANGLES) 131 130 132 72: 242 type=121 (ANGLES) 131 130 133 72: 243 type=121 (ANGLES) 132 130 133 72: 244 type=122 (ANGLES) 119 134 135 72: 245 type=123 (ANGLES) 119 134 136 72: 246 type=124 (ANGLES) 135 134 136 72: 247 type=125 (ANGLES) 134 136 137 72: 248 type=126 (ANGLES) 134 136 138 72: 249 type=127 (ANGLES) 137 136 138 72: 250 type=116 (ANGLES) 136 138 139 72: 251 type=128 (ANGLES) 136 138 140 72: 252 type=129 (ANGLES) 136 138 144 72: 253 type=118 (ANGLES) 139 138 140 72: 254 type=116 (ANGLES) 139 138 144 72: 255 type=119 (ANGLES) 140 138 144 72: 256 type=118 (ANGLES) 138 140 141 72: 257 type=118 (ANGLES) 138 140 142 72: 258 type=118 (ANGLES) 138 140 143 72: 259 type=121 (ANGLES) 141 140 142 72: 260 type=121 (ANGLES) 141 140 143 72: 261 type=121 (ANGLES) 142 140 143 72: 262 type=122 (ANGLES) 138 144 145 72: 263 type=123 (ANGLES) 138 144 146 72: 264 type=124 (ANGLES) 145 144 146 72: 265 type=125 (ANGLES) 144 146 147 72: 266 type=126 (ANGLES) 144 146 148 72: 267 type=127 (ANGLES) 147 146 148 72: 268 type=116 (ANGLES) 146 148 149 72: 269 type=128 (ANGLES) 146 148 150 72: 270 type=129 (ANGLES) 146 148 154 72: 271 type=118 (ANGLES) 149 148 150 72: 272 type=116 (ANGLES) 149 148 154 72: 273 type=119 (ANGLES) 150 148 154 72: 274 type=118 (ANGLES) 148 150 151 72: 275 type=118 (ANGLES) 148 150 152 72: 276 type=118 (ANGLES) 148 150 153 72: 277 type=121 (ANGLES) 151 150 152 72: 278 type=121 (ANGLES) 151 150 153 72: 279 type=121 (ANGLES) 152 150 153 72: 280 type=122 (ANGLES) 148 154 155 72: G96Angle: 72: nr: 0 72: Restr. Angles: 72: nr: 0 72: Lin. Angle: 72: nr: 0 72: Bond-Cross: 72: nr: 0 72: BA-Cross: 72: nr: 0 72: U-B: 72: nr: 0 72: Quartic Angles: 72: nr: 0 72: Tab. Angles: 72: nr: 0 72: Proper Dih.: 72: nr: 145 72: iatoms: 72: 0 type=140 (PDIHS) 4 24 22 23 72: 1 type=141 (PDIHS) 22 26 24 25 72: 2 type=140 (PDIHS) 26 40 38 39 72: 3 type=141 (PDIHS) 38 42 40 41 72: 4 type=140 (PDIHS) 42 60 58 59 72: 5 type=142 (PDIHS) 44 47 50 48 72: 6 type=142 (PDIHS) 47 52 48 49 72: 7 type=142 (PDIHS) 47 54 50 51 72: 8 type=142 (PDIHS) 48 56 52 53 72: 9 type=142 (PDIHS) 50 56 54 55 72: 10 type=142 (PDIHS) 52 54 56 57 72: 11 type=141 (PDIHS) 58 62 60 61 72: 12 type=140 (PDIHS) 62 67 65 66 72: 13 type=141 (PDIHS) 65 69 67 68 72: 14 type=140 (PDIHS) 69 91 89 90 72: 15 type=141 (PDIHS) 77 82 80 81 72: 16 type=140 (PDIHS) 80 83 82 86 72: 17 type=141 (PDIHS) 82 84 83 85 72: 18 type=141 (PDIHS) 82 87 86 88 72: 19 type=141 (PDIHS) 89 93 91 92 72: 20 type=140 (PDIHS) 93 102 100 101 72: 21 type=141 (PDIHS) 100 104 102 103 72: 22 type=140 (PDIHS) 104 117 115 116 72: 23 type=140 (PDIHS) 109 113 112 114 72: 24 type=141 (PDIHS) 115 119 117 118 72: 25 type=140 (PDIHS) 119 136 134 135 72: 26 type=141 (PDIHS) 134 138 136 137 72: 27 type=140 (PDIHS) 138 146 144 145 72: 28 type=141 (PDIHS) 144 148 146 147 72: Ryckaert-Bell.: 72: nr: 1565 72: iatoms: 72: 0 type=143 (RBDIHS) 1 0 4 5 72: 1 type=144 (RBDIHS) 1 0 4 6 72: 2 type=144 (RBDIHS) 1 0 4 22 72: 3 type=143 (RBDIHS) 2 0 4 5 72: 4 type=144 (RBDIHS) 2 0 4 6 72: 5 type=144 (RBDIHS) 2 0 4 22 72: 6 type=143 (RBDIHS) 3 0 4 5 72: 7 type=144 (RBDIHS) 3 0 4 6 72: 8 type=144 (RBDIHS) 3 0 4 22 72: 9 type=145 (RBDIHS) 0 4 6 9 72: 10 type=146 (RBDIHS) 22 4 6 9 72: 11 type=147 (RBDIHS) 0 4 6 7 72: 12 type=147 (RBDIHS) 0 4 6 8 72: 13 type=148 (RBDIHS) 5 4 6 7 72: 14 type=148 (RBDIHS) 5 4 6 8 72: 15 type=148 (RBDIHS) 5 4 6 9 72: 16 type=149 (RBDIHS) 22 4 6 7 72: 17 type=149 (RBDIHS) 22 4 6 8 72: 18 type=150 (RBDIHS) 0 4 22 24 72: 19 type=151 (RBDIHS) 6 4 22 24 72: 20 type=148 (RBDIHS) 4 6 9 10 72: 21 type=148 (RBDIHS) 4 6 9 11 72: 22 type=152 (RBDIHS) 4 6 9 12 72: 23 type=148 (RBDIHS) 7 6 9 10 72: 24 type=148 (RBDIHS) 7 6 9 11 72: 25 type=148 (RBDIHS) 7 6 9 12 72: 26 type=148 (RBDIHS) 8 6 9 10 72: 27 type=148 (RBDIHS) 8 6 9 11 72: 28 type=148 (RBDIHS) 8 6 9 12 72: 29 type=148 (RBDIHS) 6 9 12 13 72: 30 type=148 (RBDIHS) 6 9 12 14 72: 31 type=152 (RBDIHS) 6 9 12 15 72: 32 type=148 (RBDIHS) 10 9 12 13 72: 33 type=148 (RBDIHS) 10 9 12 14 72: 34 type=148 (RBDIHS) 10 9 12 15 72: 35 type=148 (RBDIHS) 11 9 12 13 72: 36 type=148 (RBDIHS) 11 9 12 14 72: 37 type=148 (RBDIHS) 11 9 12 15 72: 38 type=148 (RBDIHS) 9 12 15 16 72: 39 type=148 (RBDIHS) 9 12 15 17 72: 40 type=153 (RBDIHS) 9 12 15 18 72: 41 type=148 (RBDIHS) 13 12 15 16 72: 42 type=148 (RBDIHS) 13 12 15 17 72: 43 type=154 (RBDIHS) 13 12 15 18 72: 44 type=148 (RBDIHS) 14 12 15 16 72: 45 type=148 (RBDIHS) 14 12 15 17 72: 46 type=154 (RBDIHS) 14 12 15 18 72: 47 type=144 (RBDIHS) 12 15 18 19 72: 48 type=144 (RBDIHS) 12 15 18 20 72: 49 type=144 (RBDIHS) 12 15 18 21 72: 50 type=143 (RBDIHS) 16 15 18 19 72: 51 type=143 (RBDIHS) 16 15 18 20 72: 52 type=143 (RBDIHS) 16 15 18 21 72: 53 type=143 (RBDIHS) 17 15 18 19 72: 54 type=143 (RBDIHS) 17 15 18 20 72: 55 type=143 (RBDIHS) 17 15 18 21 72: 56 type=155 (RBDIHS) 4 22 24 25 72: 57 type=156 (RBDIHS) 4 22 24 26 72: 58 type=155 (RBDIHS) 23 22 24 25 72: 59 type=157 (RBDIHS) 23 22 24 26 72: 60 type=158 (RBDIHS) 22 24 26 28 72: 61 type=159 (RBDIHS) 22 24 26 38 72: 62 type=160 (RBDIHS) 24 26 28 30 72: 63 type=160 (RBDIHS) 24 26 28 34 72: 64 type=161 (RBDIHS) 38 26 28 30 72: 65 type=161 (RBDIHS) 38 26 28 34 72: 66 type=147 (RBDIHS) 24 26 28 29 72: 67 type=148 (RBDIHS) 27 26 28 29 72: 68 type=148 (RBDIHS) 27 26 28 30 72: 69 type=148 (RBDIHS) 27 26 28 34 72: 70 type=149 (RBDIHS) 38 26 28 29 72: 71 type=150 (RBDIHS) 24 26 38 40 72: 72 type=151 (RBDIHS) 28 26 38 40 72: 73 type=148 (RBDIHS) 26 28 30 31 72: 74 type=148 (RBDIHS) 26 28 30 32 72: 75 type=148 (RBDIHS) 26 28 30 33 72: 76 type=148 (RBDIHS) 29 28 30 31 72: 77 type=148 (RBDIHS) 29 28 30 32 72: 78 type=148 (RBDIHS) 29 28 30 33 72: 79 type=148 (RBDIHS) 34 28 30 31 72: 80 type=148 (RBDIHS) 34 28 30 32 72: 81 type=148 (RBDIHS) 34 28 30 33 72: 82 type=148 (RBDIHS) 26 28 34 35 72: 83 type=148 (RBDIHS) 26 28 34 36 72: 84 type=148 (RBDIHS) 26 28 34 37 72: 85 type=148 (RBDIHS) 29 28 34 35 72: 86 type=148 (RBDIHS) 29 28 34 36 72: 87 type=148 (RBDIHS) 29 28 34 37 72: 88 type=148 (RBDIHS) 30 28 34 35 72: 89 type=148 (RBDIHS) 30 28 34 36 72: 90 type=148 (RBDIHS) 30 28 34 37 72: 91 type=155 (RBDIHS) 26 38 40 41 72: 92 type=156 (RBDIHS) 26 38 40 42 72: 93 type=155 (RBDIHS) 39 38 40 41 72: 94 type=157 (RBDIHS) 39 38 40 42 72: 95 type=158 (RBDIHS) 38 40 42 44 72: 96 type=159 (RBDIHS) 38 40 42 58 72: 97 type=147 (RBDIHS) 40 42 44 45 72: 98 type=147 (RBDIHS) 40 42 44 46 72: 99 type=162 (RBDIHS) 40 42 44 47 72: 100 type=148 (RBDIHS) 43 42 44 45 72: 101 type=148 (RBDIHS) 43 42 44 46 72: 102 type=163 (RBDIHS) 43 42 44 47 72: 103 type=149 (RBDIHS) 58 42 44 45 72: 104 type=149 (RBDIHS) 58 42 44 46 72: 105 type=164 (RBDIHS) 58 42 44 47 72: 106 type=150 (RBDIHS) 40 42 58 60 72: 107 type=151 (RBDIHS) 44 42 58 60 72: 108 type=165 (RBDIHS) 44 47 48 49 72: 109 type=165 (RBDIHS) 44 47 48 52 72: 110 type=165 (RBDIHS) 50 47 48 49 72: 111 type=165 (RBDIHS) 50 47 48 52 72: 112 type=165 (RBDIHS) 44 47 50 51 72: 113 type=165 (RBDIHS) 44 47 50 54 72: 114 type=165 (RBDIHS) 48 47 50 51 72: 115 type=165 (RBDIHS) 48 47 50 54 72: 116 type=165 (RBDIHS) 47 48 52 53 72: 117 type=165 (RBDIHS) 47 48 52 56 72: 118 type=165 (RBDIHS) 49 48 52 53 72: 119 type=165 (RBDIHS) 49 48 52 56 72: 120 type=165 (RBDIHS) 47 50 54 55 72: 121 type=165 (RBDIHS) 47 50 54 56 72: 122 type=165 (RBDIHS) 51 50 54 55 72: 123 type=165 (RBDIHS) 51 50 54 56 72: 124 type=165 (RBDIHS) 48 52 56 54 72: 125 type=165 (RBDIHS) 48 52 56 57 72: 126 type=165 (RBDIHS) 53 52 56 54 72: 127 type=165 (RBDIHS) 53 52 56 57 72: 128 type=165 (RBDIHS) 50 54 56 52 72: 129 type=165 (RBDIHS) 50 54 56 57 72: 130 type=165 (RBDIHS) 55 54 56 52 72: 131 type=165 (RBDIHS) 55 54 56 57 72: 132 type=155 (RBDIHS) 42 58 60 61 72: 133 type=156 (RBDIHS) 42 58 60 62 72: 134 type=155 (RBDIHS) 59 58 60 61 72: 135 type=157 (RBDIHS) 59 58 60 62 72: 136 type=159 (RBDIHS) 58 60 62 65 72: 137 type=150 (RBDIHS) 60 62 65 67 72: 138 type=155 (RBDIHS) 62 65 67 68 72: 139 type=156 (RBDIHS) 62 65 67 69 72: 140 type=155 (RBDIHS) 66 65 67 68 72: 141 type=157 (RBDIHS) 66 65 67 69 72: 142 type=158 (RBDIHS) 65 67 69 71 72: 143 type=159 (RBDIHS) 65 67 69 89 72: 144 type=166 (RBDIHS) 67 69 71 74 72: 145 type=167 (RBDIHS) 89 69 71 74 72: 146 type=147 (RBDIHS) 67 69 71 72 72: 147 type=147 (RBDIHS) 67 69 71 73 72: 148 type=148 (RBDIHS) 70 69 71 72 72: 149 type=148 (RBDIHS) 70 69 71 73 72: 150 type=148 (RBDIHS) 70 69 71 74 72: 151 type=149 (RBDIHS) 89 69 71 72 72: 152 type=149 (RBDIHS) 89 69 71 73 72: 153 type=150 (RBDIHS) 67 69 89 91 72: 154 type=151 (RBDIHS) 71 69 89 91 72: 155 type=148 (RBDIHS) 69 71 74 75 72: 156 type=148 (RBDIHS) 69 71 74 76 72: 157 type=152 (RBDIHS) 69 71 74 77 72: 158 type=148 (RBDIHS) 72 71 74 75 72: 159 type=148 (RBDIHS) 72 71 74 76 72: 160 type=148 (RBDIHS) 72 71 74 77 72: 161 type=148 (RBDIHS) 73 71 74 75 72: 162 type=148 (RBDIHS) 73 71 74 76 72: 163 type=148 (RBDIHS) 73 71 74 77 72: 164 type=148 (RBDIHS) 71 74 77 78 72: 165 type=148 (RBDIHS) 71 74 77 79 72: 166 type=153 (RBDIHS) 71 74 77 80 72: 167 type=148 (RBDIHS) 75 74 77 78 72: 168 type=148 (RBDIHS) 75 74 77 79 72: 169 type=168 (RBDIHS) 75 74 77 80 72: 170 type=148 (RBDIHS) 76 74 77 78 72: 171 type=148 (RBDIHS) 76 74 77 79 72: 172 type=168 (RBDIHS) 76 74 77 80 72: 173 type=169 (RBDIHS) 74 77 80 81 72: 174 type=170 (RBDIHS) 74 77 80 82 72: 175 type=171 (RBDIHS) 78 77 80 82 72: 176 type=171 (RBDIHS) 79 77 80 82 72: 177 type=172 (RBDIHS) 77 80 82 83 72: 178 type=172 (RBDIHS) 77 80 82 86 72: 179 type=173 (RBDIHS) 81 80 82 83 72: 180 type=173 (RBDIHS) 81 80 82 86 72: 181 type=173 (RBDIHS) 80 82 83 84 72: 182 type=173 (RBDIHS) 80 82 83 85 72: 183 type=173 (RBDIHS) 86 82 83 84 72: 184 type=173 (RBDIHS) 86 82 83 85 72: 185 type=173 (RBDIHS) 80 82 86 87 72: 186 type=173 (RBDIHS) 80 82 86 88 72: 187 type=173 (RBDIHS) 83 82 86 87 72: 188 type=173 (RBDIHS) 83 82 86 88 72: 189 type=155 (RBDIHS) 69 89 91 92 72: 190 type=156 (RBDIHS) 69 89 91 93 72: 191 type=155 (RBDIHS) 90 89 91 92 72: 192 type=157 (RBDIHS) 90 89 91 93 72: 193 type=158 (RBDIHS) 89 91 93 95 72: 194 type=159 (RBDIHS) 89 91 93 100 72: 195 type=174 (RBDIHS) 91 93 95 98 72: 196 type=175 (RBDIHS) 100 93 95 98 72: 197 type=147 (RBDIHS) 91 93 95 96 72: 198 type=147 (RBDIHS) 91 93 95 97 72: 199 type=148 (RBDIHS) 94 93 95 96 72: 200 type=148 (RBDIHS) 94 93 95 97 72: 201 type=176 (RBDIHS) 94 93 95 98 72: 202 type=149 (RBDIHS) 100 93 95 96 72: 203 type=149 (RBDIHS) 100 93 95 97 72: 204 type=150 (RBDIHS) 91 93 100 102 72: 205 type=151 (RBDIHS) 95 93 100 102 72: 206 type=177 (RBDIHS) 93 95 98 99 72: 207 type=178 (RBDIHS) 96 95 98 99 72: 208 type=178 (RBDIHS) 97 95 98 99 72: 209 type=155 (RBDIHS) 93 100 102 103 72: 210 type=156 (RBDIHS) 93 100 102 104 72: 211 type=155 (RBDIHS) 101 100 102 103 72: 212 type=157 (RBDIHS) 101 100 102 104 72: 213 type=158 (RBDIHS) 100 102 104 106 72: 214 type=159 (RBDIHS) 100 102 104 115 72: 215 type=179 (RBDIHS) 102 104 106 109 72: 216 type=180 (RBDIHS) 115 104 106 109 72: 217 type=147 (RBDIHS) 102 104 106 107 72: 218 type=147 (RBDIHS) 102 104 106 108 72: 219 type=148 (RBDIHS) 105 104 106 107 72: 220 type=148 (RBDIHS) 105 104 106 108 72: 221 type=148 (RBDIHS) 105 104 106 109 72: 222 type=149 (RBDIHS) 115 104 106 107 72: 223 type=149 (RBDIHS) 115 104 106 108 72: 224 type=150 (RBDIHS) 102 104 115 117 72: 225 type=151 (RBDIHS) 106 104 115 117 72: 226 type=148 (RBDIHS) 104 106 109 110 72: 227 type=148 (RBDIHS) 104 106 109 111 72: 228 type=181 (RBDIHS) 104 106 109 112 72: 229 type=148 (RBDIHS) 107 106 109 110 72: 230 type=148 (RBDIHS) 107 106 109 111 72: 231 type=182 (RBDIHS) 107 106 109 112 72: 232 type=148 (RBDIHS) 108 106 109 110 72: 233 type=148 (RBDIHS) 108 106 109 111 72: 234 type=182 (RBDIHS) 108 106 109 112 72: 235 type=183 (RBDIHS) 106 109 112 113 72: 236 type=183 (RBDIHS) 106 109 112 114 72: 237 type=155 (RBDIHS) 104 115 117 118 72: 238 type=156 (RBDIHS) 104 115 117 119 72: 239 type=155 (RBDIHS) 116 115 117 118 72: 240 type=157 (RBDIHS) 116 115 117 119 72: 241 type=158 (RBDIHS) 115 117 119 121 72: 242 type=159 (RBDIHS) 115 117 119 134 72: 243 type=184 (RBDIHS) 117 119 121 124 72: 244 type=185 (RBDIHS) 134 119 121 124 72: 245 type=147 (RBDIHS) 117 119 121 122 72: 246 type=147 (RBDIHS) 117 119 121 123 72: 247 type=148 (RBDIHS) 120 119 121 122 72: 248 type=148 (RBDIHS) 120 119 121 123 72: 249 type=148 (RBDIHS) 120 119 121 124 72: 250 type=149 (RBDIHS) 134 119 121 122 72: 251 type=149 (RBDIHS) 134 119 121 123 72: 252 type=150 (RBDIHS) 117 119 134 136 72: 253 type=151 (RBDIHS) 121 119 134 136 72: 254 type=148 (RBDIHS) 119 121 124 125 72: 255 type=152 (RBDIHS) 119 121 124 126 72: 256 type=152 (RBDIHS) 119 121 124 130 72: 257 type=148 (RBDIHS) 122 121 124 125 72: 258 type=148 (RBDIHS) 122 121 124 126 72: 259 type=148 (RBDIHS) 122 121 124 130 72: 260 type=148 (RBDIHS) 123 121 124 125 72: 261 type=148 (RBDIHS) 123 121 124 126 72: 262 type=148 (RBDIHS) 123 121 124 130 72: 263 type=148 (RBDIHS) 121 124 126 127 72: 264 type=148 (RBDIHS) 121 124 126 128 72: 265 type=148 (RBDIHS) 121 124 126 129 72: 266 type=148 (RBDIHS) 125 124 126 127 72: 267 type=148 (RBDIHS) 125 124 126 128 72: 268 type=148 (RBDIHS) 125 124 126 129 72: 269 type=148 (RBDIHS) 130 124 126 127 72: 270 type=148 (RBDIHS) 130 124 126 128 72: 271 type=148 (RBDIHS) 130 124 126 129 72: 272 type=148 (RBDIHS) 121 124 130 131 72: 273 type=148 (RBDIHS) 121 124 130 132 72: 274 type=148 (RBDIHS) 121 124 130 133 72: 275 type=148 (RBDIHS) 125 124 130 131 72: 276 type=148 (RBDIHS) 125 124 130 132 72: 277 type=148 (RBDIHS) 125 124 130 133 72: 278 type=148 (RBDIHS) 126 124 130 131 72: 279 type=148 (RBDIHS) 126 124 130 132 72: 280 type=148 (RBDIHS) 126 124 130 133 72: 281 type=155 (RBDIHS) 119 134 136 137 72: 282 type=156 (RBDIHS) 119 134 136 138 72: 283 type=155 (RBDIHS) 135 134 136 137 72: 284 type=157 (RBDIHS) 135 134 136 138 72: 285 type=158 (RBDIHS) 134 136 138 140 72: 286 type=159 (RBDIHS) 134 136 138 144 72: 287 type=147 (RBDIHS) 136 138 140 141 72: 288 type=147 (RBDIHS) 136 138 140 142 72: 289 type=147 (RBDIHS) 136 138 140 143 72: 290 type=148 (RBDIHS) 139 138 140 141 72: 291 type=148 (RBDIHS) 139 138 140 142 72: 292 type=148 (RBDIHS) 139 138 140 143 72: 293 type=149 (RBDIHS) 144 138 140 141 72: 294 type=149 (RBDIHS) 144 138 140 142 72: 295 type=149 (RBDIHS) 144 138 140 143 72: 296 type=150 (RBDIHS) 136 138 144 146 72: 297 type=151 (RBDIHS) 140 138 144 146 72: 298 type=155 (RBDIHS) 138 144 146 147 72: 299 type=156 (RBDIHS) 138 144 146 148 72: 300 type=155 (RBDIHS) 145 144 146 147 72: 301 type=157 (RBDIHS) 145 144 146 148 72: 302 type=158 (RBDIHS) 144 146 148 150 72: 303 type=159 (RBDIHS) 144 146 148 154 72: 304 type=147 (RBDIHS) 146 148 150 151 72: 305 type=147 (RBDIHS) 146 148 150 152 72: 306 type=147 (RBDIHS) 146 148 150 153 72: 307 type=148 (RBDIHS) 149 148 150 151 72: 308 type=148 (RBDIHS) 149 148 150 152 72: 309 type=148 (RBDIHS) 149 148 150 153 72: 310 type=149 (RBDIHS) 154 148 150 151 72: 311 type=149 (RBDIHS) 154 148 150 152 72: 312 type=149 (RBDIHS) 154 148 150 153 72: Restr. Dih.: 72: nr: 0 72: CBT Dih.: 72: nr: 0 72: Fourier Dih.: 72: nr: 0 72: Improper Dih.: 72: nr: 0 72: Per. Imp. Dih.: 72: nr: 0 72: Tab. Dih.: 72: nr: 0 72: CMAP Dih.: 72: nr: 0 72: GB 1-2 Pol.: 72: nr: 0 72: GB 1-3 Pol.: 72: nr: 0 72: GB 1-4 Pol.: 72: nr: 0 72: GB Polariz.: 72: nr: 0 72: Nonpolar Sol.: 72: nr: 0 72: LJ-14: 72: nr: 1197 72: iatoms: 72: 0 type=186 (LJ14) 0 7 72: 1 type=186 (LJ14) 0 8 72: 2 type=187 (LJ14) 0 9 72: 3 type=188 (LJ14) 0 23 72: 4 type=189 (LJ14) 0 24 72: 5 type=190 (LJ14) 1 5 72: 6 type=190 (LJ14) 1 6 72: 7 type=190 (LJ14) 1 22 72: 8 type=190 (LJ14) 2 5 72: 9 type=190 (LJ14) 2 6 72: 10 type=190 (LJ14) 2 22 72: 11 type=190 (LJ14) 3 5 72: 12 type=190 (LJ14) 3 6 72: 13 type=190 (LJ14) 3 22 72: 14 type=191 (LJ14) 4 10 72: 15 type=191 (LJ14) 4 11 72: 16 type=192 (LJ14) 4 12 72: 17 type=190 (LJ14) 4 25 72: 18 type=192 (LJ14) 4 26 72: 19 type=193 (LJ14) 5 7 72: 20 type=193 (LJ14) 5 8 72: 21 type=191 (LJ14) 5 9 72: 22 type=194 (LJ14) 5 23 72: 23 type=186 (LJ14) 5 24 72: 24 type=191 (LJ14) 6 13 72: 25 type=191 (LJ14) 6 14 72: 26 type=192 (LJ14) 6 15 72: 27 type=195 (LJ14) 6 23 72: 28 type=187 (LJ14) 6 24 72: 29 type=193 (LJ14) 7 10 72: 30 type=193 (LJ14) 7 11 72: 31 type=191 (LJ14) 7 12 72: 32 type=196 (LJ14) 7 22 72: 33 type=193 (LJ14) 8 10 72: 34 type=193 (LJ14) 8 11 72: 35 type=191 (LJ14) 8 12 72: 36 type=196 (LJ14) 8 22 72: 37 type=191 (LJ14) 9 16 72: 38 type=191 (LJ14) 9 17 72: 39 type=187 (LJ14) 9 18 72: 40 type=197 (LJ14) 9 22 72: 41 type=193 (LJ14) 10 13 72: 42 type=193 (LJ14) 10 14 72: 43 type=191 (LJ14) 10 15 72: 44 type=193 (LJ14) 11 13 72: 45 type=193 (LJ14) 11 14 72: 46 type=191 (LJ14) 11 15 72: 47 type=190 (LJ14) 12 19 72: 48 type=190 (LJ14) 12 20 72: 49 type=190 (LJ14) 12 21 72: 50 type=193 (LJ14) 13 16 72: 51 type=193 (LJ14) 13 17 72: 52 type=186 (LJ14) 13 18 72: 53 type=193 (LJ14) 14 16 72: 54 type=193 (LJ14) 14 17 72: 55 type=186 (LJ14) 14 18 72: 56 type=190 (LJ14) 16 19 72: 57 type=190 (LJ14) 16 20 72: 58 type=190 (LJ14) 16 21 72: 59 type=190 (LJ14) 17 19 72: 60 type=190 (LJ14) 17 20 72: 61 type=190 (LJ14) 17 21 72: 62 type=196 (LJ14) 22 27 72: 63 type=197 (LJ14) 22 28 72: 64 type=198 (LJ14) 22 38 72: 65 type=190 (LJ14) 23 25 72: 66 type=195 (LJ14) 23 26 72: 67 type=186 (LJ14) 24 29 72: 68 type=187 (LJ14) 24 30 72: 69 type=187 (LJ14) 24 34 72: 70 type=188 (LJ14) 24 39 72: 71 type=189 (LJ14) 24 40 72: 72 type=190 (LJ14) 25 27 72: 73 type=190 (LJ14) 25 28 72: 74 type=190 (LJ14) 25 38 72: 75 type=191 (LJ14) 26 31 72: 76 type=191 (LJ14) 26 32 72: 77 type=191 (LJ14) 26 33 72: 78 type=191 (LJ14) 26 35 72: 79 type=191 (LJ14) 26 36 72: 80 type=191 (LJ14) 26 37 72: 81 type=190 (LJ14) 26 41 72: 82 type=192 (LJ14) 26 42 72: 83 type=193 (LJ14) 27 29 72: 84 type=191 (LJ14) 27 30 72: 85 type=191 (LJ14) 27 34 72: 86 type=194 (LJ14) 27 39 72: 87 type=186 (LJ14) 27 40 72: 88 type=195 (LJ14) 28 39 72: 89 type=187 (LJ14) 28 40 72: 90 type=193 (LJ14) 29 31 72: 91 type=193 (LJ14) 29 32 72: 92 type=193 (LJ14) 29 33 72: 93 type=193 (LJ14) 29 35 72: 94 type=193 (LJ14) 29 36 72: 95 type=193 (LJ14) 29 37 72: 96 type=196 (LJ14) 29 38 72: 97 type=191 (LJ14) 30 35 72: 98 type=191 (LJ14) 30 36 72: 99 type=191 (LJ14) 30 37 72: 100 type=197 (LJ14) 30 38 72: 101 type=191 (LJ14) 31 34 72: 102 type=191 (LJ14) 32 34 72: 103 type=191 (LJ14) 33 34 72: 104 type=197 (LJ14) 34 38 72: 105 type=196 (LJ14) 38 43 72: 106 type=197 (LJ14) 38 44 72: 107 type=198 (LJ14) 38 58 72: 108 type=190 (LJ14) 39 41 72: 109 type=195 (LJ14) 39 42 72: 110 type=186 (LJ14) 40 45 72: 111 type=186 (LJ14) 40 46 72: 112 type=199 (LJ14) 40 47 72: 113 type=188 (LJ14) 40 59 72: 114 type=189 (LJ14) 40 60 72: 115 type=190 (LJ14) 41 43 72: 116 type=190 (LJ14) 41 44 72: 117 type=190 (LJ14) 41 58 72: 118 type=200 (LJ14) 42 48 72: 119 type=200 (LJ14) 42 50 72: 120 type=190 (LJ14) 42 61 72: 121 type=192 (LJ14) 42 62 72: 122 type=193 (LJ14) 43 45 72: 123 type=193 (LJ14) 43 46 72: 124 type=201 (LJ14) 43 47 72: 125 type=194 (LJ14) 43 59 72: 126 type=186 (LJ14) 43 60 72: 127 type=202 (LJ14) 44 49 72: 128 type=202 (LJ14) 44 51 72: 129 type=200 (LJ14) 44 52 72: 130 type=200 (LJ14) 44 54 72: 131 type=195 (LJ14) 44 59 72: 132 type=187 (LJ14) 44 60 72: 133 type=201 (LJ14) 45 48 72: 134 type=201 (LJ14) 45 50 72: 135 type=196 (LJ14) 45 58 72: 136 type=201 (LJ14) 46 48 72: 137 type=201 (LJ14) 46 50 72: 138 type=196 (LJ14) 46 58 72: 139 type=203 (LJ14) 47 53 72: 140 type=203 (LJ14) 47 55 72: 141 type=204 (LJ14) 47 56 72: 142 type=205 (LJ14) 47 58 72: 143 type=203 (LJ14) 48 51 72: 144 type=204 (LJ14) 48 54 72: 145 type=203 (LJ14) 48 57 72: 146 type=203 (LJ14) 49 50 72: 147 type=206 (LJ14) 49 53 72: 148 type=203 (LJ14) 49 56 72: 149 type=204 (LJ14) 50 52 72: 150 type=203 (LJ14) 50 57 72: 151 type=206 (LJ14) 51 55 72: 152 type=203 (LJ14) 51 56 72: 153 type=203 (LJ14) 52 55 72: 154 type=203 (LJ14) 53 54 72: 155 type=206 (LJ14) 53 57 72: 156 type=206 (LJ14) 55 57 72: 157 type=196 (LJ14) 58 63 72: 158 type=196 (LJ14) 58 64 72: 159 type=198 (LJ14) 58 65 72: 160 type=190 (LJ14) 59 61 72: 161 type=195 (LJ14) 59 62 72: 162 type=188 (LJ14) 60 66 72: 163 type=189 (LJ14) 60 67 72: 164 type=190 (LJ14) 61 63 72: 165 type=190 (LJ14) 61 64 72: 166 type=190 (LJ14) 61 65 72: 167 type=190 (LJ14) 62 68 72: 168 type=192 (LJ14) 62 69 72: 169 type=194 (LJ14) 63 66 72: 170 type=186 (LJ14) 63 67 72: 171 type=194 (LJ14) 64 66 72: 172 type=186 (LJ14) 64 67 72: 173 type=196 (LJ14) 65 70 72: 174 type=197 (LJ14) 65 71 72: 175 type=198 (LJ14) 65 89 72: 176 type=190 (LJ14) 66 68 72: 177 type=195 (LJ14) 66 69 72: 178 type=186 (LJ14) 67 72 72: 179 type=186 (LJ14) 67 73 72: 180 type=187 (LJ14) 67 74 72: 181 type=188 (LJ14) 67 90 72: 182 type=189 (LJ14) 67 91 72: 183 type=190 (LJ14) 68 70 72: 184 type=190 (LJ14) 68 71 72: 185 type=190 (LJ14) 68 89 72: 186 type=191 (LJ14) 69 75 72: 187 type=191 (LJ14) 69 76 72: 188 type=192 (LJ14) 69 77 72: 189 type=190 (LJ14) 69 92 72: 190 type=192 (LJ14) 69 93 72: 191 type=193 (LJ14) 70 72 72: 192 type=193 (LJ14) 70 73 72: 193 type=191 (LJ14) 70 74 72: 194 type=194 (LJ14) 70 90 72: 195 type=186 (LJ14) 70 91 72: 196 type=191 (LJ14) 71 78 72: 197 type=191 (LJ14) 71 79 72: 198 type=187 (LJ14) 71 80 72: 199 type=195 (LJ14) 71 90 72: 200 type=187 (LJ14) 71 91 72: 201 type=193 (LJ14) 72 75 72: 202 type=193 (LJ14) 72 76 72: 203 type=191 (LJ14) 72 77 72: 204 type=196 (LJ14) 72 89 72: 205 type=193 (LJ14) 73 75 72: 206 type=193 (LJ14) 73 76 72: 207 type=191 (LJ14) 73 77 72: 208 type=196 (LJ14) 73 89 72: 209 type=190 (LJ14) 74 81 72: 210 type=207 (LJ14) 74 82 72: 211 type=197 (LJ14) 74 89 72: 212 type=193 (LJ14) 75 78 72: 213 type=193 (LJ14) 75 79 72: 214 type=186 (LJ14) 75 80 72: 215 type=193 (LJ14) 76 78 72: 216 type=193 (LJ14) 76 79 72: 217 type=186 (LJ14) 76 80 72: 218 type=187 (LJ14) 77 83 72: 219 type=187 (LJ14) 77 86 72: 220 type=190 (LJ14) 78 81 72: 221 type=208 (LJ14) 78 82 72: 222 type=190 (LJ14) 79 81 72: 223 type=208 (LJ14) 79 82 72: 224 type=190 (LJ14) 80 84 72: 225 type=190 (LJ14) 80 85 72: 226 type=190 (LJ14) 80 87 72: 227 type=190 (LJ14) 80 88 72: 228 type=190 (LJ14) 81 83 72: 229 type=190 (LJ14) 81 86 72: 230 type=190 (LJ14) 83 87 72: 231 type=190 (LJ14) 83 88 72: 232 type=190 (LJ14) 84 86 72: 233 type=190 (LJ14) 85 86 72: 234 type=196 (LJ14) 89 94 72: 235 type=197 (LJ14) 89 95 72: 236 type=198 (LJ14) 89 100 72: 237 type=190 (LJ14) 90 92 72: 238 type=195 (LJ14) 90 93 72: 239 type=186 (LJ14) 91 96 72: 240 type=186 (LJ14) 91 97 72: 241 type=209 (LJ14) 91 98 72: 242 type=188 (LJ14) 91 101 72: 243 type=189 (LJ14) 91 102 72: 244 type=190 (LJ14) 92 94 72: 245 type=190 (LJ14) 92 95 72: 246 type=190 (LJ14) 92 100 72: 247 type=190 (LJ14) 93 99 72: 248 type=190 (LJ14) 93 103 72: 249 type=192 (LJ14) 93 104 72: 250 type=193 (LJ14) 94 96 72: 251 type=193 (LJ14) 94 97 72: 252 type=210 (LJ14) 94 98 72: 253 type=194 (LJ14) 94 101 72: 254 type=186 (LJ14) 94 102 72: 255 type=195 (LJ14) 95 101 72: 256 type=187 (LJ14) 95 102 72: 257 type=190 (LJ14) 96 99 72: 258 type=196 (LJ14) 96 100 72: 259 type=190 (LJ14) 97 99 72: 260 type=196 (LJ14) 97 100 72: 261 type=211 (LJ14) 98 100 72: 262 type=196 (LJ14) 100 105 72: 263 type=197 (LJ14) 100 106 72: 264 type=198 (LJ14) 100 115 72: 265 type=190 (LJ14) 101 103 72: 266 type=195 (LJ14) 101 104 72: 267 type=186 (LJ14) 102 107 72: 268 type=186 (LJ14) 102 108 72: 269 type=187 (LJ14) 102 109 72: 270 type=188 (LJ14) 102 116 72: 271 type=189 (LJ14) 102 117 72: 272 type=190 (LJ14) 103 105 72: 273 type=190 (LJ14) 103 106 72: 274 type=190 (LJ14) 103 115 72: 275 type=191 (LJ14) 104 110 72: 276 type=191 (LJ14) 104 111 72: 277 type=197 (LJ14) 104 112 72: 278 type=190 (LJ14) 104 118 72: 279 type=192 (LJ14) 104 119 72: 280 type=193 (LJ14) 105 107 72: 281 type=193 (LJ14) 105 108 72: 282 type=191 (LJ14) 105 109 72: 283 type=194 (LJ14) 105 116 72: 284 type=186 (LJ14) 105 117 72: 285 type=195 (LJ14) 106 113 72: 286 type=195 (LJ14) 106 114 72: 287 type=195 (LJ14) 106 116 72: 288 type=187 (LJ14) 106 117 72: 289 type=193 (LJ14) 107 110 72: 290 type=193 (LJ14) 107 111 72: 291 type=196 (LJ14) 107 112 72: 292 type=196 (LJ14) 107 115 72: 293 type=193 (LJ14) 108 110 72: 294 type=193 (LJ14) 108 111 72: 295 type=196 (LJ14) 108 112 72: 296 type=196 (LJ14) 108 115 72: 297 type=197 (LJ14) 109 115 72: 298 type=194 (LJ14) 110 113 72: 299 type=194 (LJ14) 110 114 72: 300 type=194 (LJ14) 111 113 72: 301 type=194 (LJ14) 111 114 72: 302 type=196 (LJ14) 115 120 72: 303 type=197 (LJ14) 115 121 72: 304 type=198 (LJ14) 115 134 72: 305 type=190 (LJ14) 116 118 72: 306 type=195 (LJ14) 116 119 72: 307 type=186 (LJ14) 117 122 72: 308 type=186 (LJ14) 117 123 72: 309 type=187 (LJ14) 117 124 72: 310 type=188 (LJ14) 117 135 72: 311 type=189 (LJ14) 117 136 72: 312 type=190 (LJ14) 118 120 72: 313 type=190 (LJ14) 118 121 72: 314 type=190 (LJ14) 118 134 72: 315 type=191 (LJ14) 119 125 72: 316 type=192 (LJ14) 119 126 72: 317 type=192 (LJ14) 119 130 72: 318 type=190 (LJ14) 119 137 72: 319 type=192 (LJ14) 119 138 72: 320 type=193 (LJ14) 120 122 72: 321 type=193 (LJ14) 120 123 72: 322 type=191 (LJ14) 120 124 72: 323 type=194 (LJ14) 120 135 72: 324 type=186 (LJ14) 120 136 72: 325 type=191 (LJ14) 121 127 72: 326 type=191 (LJ14) 121 128 72: 327 type=191 (LJ14) 121 129 72: 328 type=191 (LJ14) 121 131 72: 329 type=191 (LJ14) 121 132 72: 330 type=191 (LJ14) 121 133 72: 331 type=195 (LJ14) 121 135 72: 332 type=187 (LJ14) 121 136 72: 333 type=193 (LJ14) 122 125 72: 334 type=191 (LJ14) 122 126 72: 335 type=191 (LJ14) 122 130 72: 336 type=196 (LJ14) 122 134 72: 337 type=193 (LJ14) 123 125 72: 338 type=191 (LJ14) 123 126 72: 339 type=191 (LJ14) 123 130 72: 340 type=196 (LJ14) 123 134 72: 341 type=197 (LJ14) 124 134 72: 342 type=193 (LJ14) 125 127 72: 343 type=193 (LJ14) 125 128 72: 344 type=193 (LJ14) 125 129 72: 345 type=193 (LJ14) 125 131 72: 346 type=193 (LJ14) 125 132 72: 347 type=193 (LJ14) 125 133 72: 348 type=191 (LJ14) 126 131 72: 349 type=191 (LJ14) 126 132 72: 350 type=191 (LJ14) 126 133 72: 351 type=191 (LJ14) 127 130 72: 352 type=191 (LJ14) 128 130 72: 353 type=191 (LJ14) 129 130 72: 354 type=196 (LJ14) 134 139 72: 355 type=197 (LJ14) 134 140 72: 356 type=198 (LJ14) 134 144 72: 357 type=190 (LJ14) 135 137 72: 358 type=195 (LJ14) 135 138 72: 359 type=186 (LJ14) 136 141 72: 360 type=186 (LJ14) 136 142 72: 361 type=186 (LJ14) 136 143 72: 362 type=188 (LJ14) 136 145 72: 363 type=189 (LJ14) 136 146 72: 364 type=190 (LJ14) 137 139 72: 365 type=190 (LJ14) 137 140 72: 366 type=190 (LJ14) 137 144 72: 367 type=190 (LJ14) 138 147 72: 368 type=192 (LJ14) 138 148 72: 369 type=193 (LJ14) 139 141 72: 370 type=193 (LJ14) 139 142 72: 371 type=193 (LJ14) 139 143 72: 372 type=194 (LJ14) 139 145 72: 373 type=186 (LJ14) 139 146 72: 374 type=195 (LJ14) 140 145 72: 375 type=187 (LJ14) 140 146 72: 376 type=196 (LJ14) 141 144 72: 377 type=196 (LJ14) 142 144 72: 378 type=196 (LJ14) 143 144 72: 379 type=196 (LJ14) 144 149 72: 380 type=197 (LJ14) 144 150 72: 381 type=198 (LJ14) 144 154 72: 382 type=190 (LJ14) 145 147 72: 383 type=195 (LJ14) 145 148 72: 384 type=186 (LJ14) 146 151 72: 385 type=186 (LJ14) 146 152 72: 386 type=186 (LJ14) 146 153 72: 387 type=188 (LJ14) 146 155 72: 388 type=190 (LJ14) 147 149 72: 389 type=190 (LJ14) 147 150 72: 390 type=190 (LJ14) 147 154 72: 391 type=193 (LJ14) 149 151 72: 392 type=193 (LJ14) 149 152 72: 393 type=193 (LJ14) 149 153 72: 394 type=194 (LJ14) 149 155 72: 395 type=195 (LJ14) 150 155 72: 396 type=196 (LJ14) 151 154 72: 397 type=196 (LJ14) 152 154 72: 398 type=196 (LJ14) 153 154 72: Coulomb-14: 72: nr: 0 72: LJC-14 q: 72: nr: 0 72: LJC Pairs NB: 72: nr: 0 72: LJ (SR): 72: nr: 0 72: Buck.ham (SR): 72: nr: 0 72: LJ: 72: nr: 0 72: B.ham: 72: nr: 0 72: Disper. corr.: 72: nr: 0 72: Coulomb (SR): 72: nr: 0 72: Coul: 72: nr: 0 72: RF excl.: 72: nr: 0 72: Coul. recip.: 72: nr: 0 72: LJ recip.: 72: nr: 0 72: DPD: 72: nr: 0 72: Polarization: 72: nr: 0 72: Water Pol.: 72: nr: 0 72: Thole Pol.: 72: nr: 0 72: Anharm. Pol.: 72: nr: 0 72: Position Rest.: 72: nr: 0 72: Flat-b. P-R.: 72: nr: 0 72: Dis. Rest.: 72: nr: 0 72: D.R.Viol. (nm): 72: nr: 0 72: Orient. Rest.: 72: nr: 0 72: Ori. R. RMSD: 72: nr: 0 72: Angle Rest.: 72: nr: 0 72: Angle Rest. Z: 72: nr: 0 72: Dih. Rest.: 72: nr: 0 72: Dih. Rest. Vi.: 72: nr: 0 72: Constraint: 72: nr: 0 72: Constr. No Co.: 72: nr: 0 72: Settle: 72: nr: 0 72: Virtual site 1: 72: nr: 0 72: Virtual site 2: 72: nr: 0 72: Virt. site 2fd: 72: nr: 0 72: Virtual site 3: 72: nr: 0 72: Virt. site 3fd: 72: nr: 0 72: Vir. site 3fad: 72: nr: 0 72: Vir. site 3out: 72: nr: 0 72: Virt. site 4fd: 72: nr: 0 72: Vir. site 4fdn: 72: nr: 0 72: Virtual site N: 72: nr: 0 72: COM Pull En.: 72: nr: 0 72: Dens. fitting: 72: nr: 0 72: Quantum En.: 72: nr: 0 72: NN Potential: 72: nr: 0 72: Potential: 72: nr: 0 72: Kinetic En.: 72: nr: 0 72: Total Energy: 72: nr: 0 72: Conserved En.: 72: nr: 0 72: Temperature: 72: nr: 0 72: Vir. Temp.: 72: nr: 0 72: Pres. DC: 72: nr: 0 72: Pressure: 72: nr: 0 72: dH/dl constr.: 72: nr: 0 72: dVremain/dl: 72: nr: 0 72: dEkin/dl: 72: nr: 0 72: dVcoul/dl: 72: nr: 0 72: dVvdw/dl: 72: nr: 0 72: dVbonded/dl: 72: nr: 0 72: dVrestraint/dl: 72: nr: 0 72: dVtemp/dl: 72: nr: 0 72: grp[T-Coupling ] nr=1, name=[ rest] 72: grp[Energy Mon. ] nr=1, name=[ rest] 72: grp[Acc. not used] nr=1, name=[ rest] 72: grp[Freeze ] nr=1, name=[ rest] 72: grp[User1 ] nr=1, name=[ rest] 72: grp[User2 ] nr=1, name=[ rest] 72: grp[VCM ] nr=1, name=[ rest] 72: grp[Compressed X] nr=1, name=[ rest] 72: grp[Or. Res. Fit] nr=1, name=[ rest] 72: grp[QMMM ] nr=1, name=[ rest] 72: grpname (11): 72: grpname[0]={name="System"} 72: grpname[1]={name="Protein"} 72: grpname[2]={name="Protein-H"} 72: grpname[3]={name="C-alpha"} 72: grpname[4]={name="Backbone"} 72: grpname[5]={name="MainChain"} 72: grpname[6]={name="MainChain+Cb"} 72: grpname[7]={name="MainChain+H"} 72: grpname[8]={name="SideChain"} 72: grpname[9]={name="SideChain-H"} 72: grpname[10]={name="rest"} 72: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 72: allocated 0 0 0 0 0 0 0 0 0 0 72: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 72: box (3x3): 72: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 72: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 72: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 72: box_rel (3x3): 72: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv (3x3): 72: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev (3x3): 72: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev (3x3): 72: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev (3x3): 72: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: nosehoover_xi: not available 72: x (156x3): 72: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 72: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 72: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 72: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 72: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 72: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 72: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 72: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 72: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 72: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 72: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 72: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 72: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 72: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 72: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 72: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 72: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 72: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 72: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 72: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 72: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 72: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 72: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 72: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 72: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 72: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 72: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 72: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 72: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 72: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 72: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 72: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 72: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 72: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 72: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 72: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 72: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 72: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 72: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 72: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 72: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 72: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 72: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 72: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 72: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 72: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 72: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 72: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 72: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 72: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 72: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 72: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 72: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 72: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 72: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 72: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 72: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 72: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 72: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 72: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 72: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 72: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 72: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 72: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 72: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 72: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 72: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 72: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 72: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 72: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 72: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 72: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 72: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 72: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 72: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 72: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 72: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 72: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 72: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 72: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 72: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 72: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 72: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 72: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 72: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 72: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 72: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 72: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 72: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 72: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 72: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 72: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 72: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 72: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 72: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 72: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 72: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 72: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 72: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 72: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 72: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 72: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 72: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 72: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 72: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 72: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 72: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 72: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 72: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 72: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 72: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 72: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 72: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 72: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 72: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 72: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 72: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 72: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 72: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 72: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 72: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 72: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 72: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 72: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 72: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 72: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 72: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 72: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 72: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 72: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 72: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 72: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 72: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 72: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 72: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 72: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 72: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 72: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 72: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 72: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 72: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 72: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 72: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 72: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 72: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 72: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 72: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 72: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 72: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 72: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 72: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 72: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 72: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 72: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 72: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 72: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 72: v (156x3): 72: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 72: Group statistics 72: T-Coupling : 156 (total 156 atoms) 72: Energy Mon. : 156 (total 156 atoms) 72: Acc. not used: 156 (total 156 atoms) 72: Freeze : 156 (total 156 atoms) 72: User1 : 156 (total 156 atoms) 72: User2 : 156 (total 156 atoms) 72: VCM : 156 (total 156 atoms) 72: Compressed X: 156 (total 156 atoms) 72: Or. Res. Fit: 156 (total 156 atoms) 72: QMMM : 156 (total 156 atoms) 72: [ OK ] DumpTest.WorksWithTpr (12 ms) 72: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 72: [----------] 2 tests from DumpTest (13 ms total) 72: 72: [----------] 3 tests from HelpwritingTest 72: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 72: [ OK ] HelpwritingTest.ConvertTprWritesHelp (1 ms) 72: [ RUN ] HelpwritingTest.DumpWritesHelp 72: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 72: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 72: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms) 72: [----------] 3 tests from HelpwritingTest (2 ms total) 72: 72: [----------] 7 tests from GmxMakeNdx 72: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 16 Protein residues 72: Analysing Protein... 72: 72: 0 System : 256 atoms 72: 1 Protein : 256 atoms 72: 2 Protein-H : 139 atoms 72: 3 C-alpha : 16 atoms 72: 4 Backbone : 48 atoms 72: 5 MainChain : 63 atoms 72: 6 MainChain+Cb : 78 atoms 72: 7 MainChain+H : 81 atoms 72: 8 SideChain : 175 atoms 72: 9 SideChain-H : 76 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (3 ms) 72: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 1 'Protein' 72: Copied index group 2 'Protein-H' 72: Merged two groups with OR: 22 10 -> 22 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNoStructureInput (5 ms) 72: [ RUN ] GmxMakeNdx.HandlesNotProtein 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesNotProtein (1 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 72: Going to read 1 old index file(s) 72: Deducing 22 atoms in the system from indices in the index file 72: 72: 0 System : 22 atoms 72: 1 Protein : 22 atoms 72: 2 Protein-H : 10 atoms 72: 3 C-alpha : 1 atoms 72: 4 Backbone : 5 atoms 72: 5 MainChain : 7 atoms 72: 6 MainChain+Cb : 8 atoms 72: 7 MainChain+H : 9 atoms 72: 8 SideChain : 13 atoms 72: 9 SideChain-H : 3 atoms 72: 10 CA : 1 atoms 72: 11 C_&_r_1 : 1 atoms 72: 12 C_&_r_2 : 1 atoms 72: 13 N_&_r_2 : 1 atoms 72: 14 N_&_r_3 : 1 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Copied index group 4 'Backbone' 72: Copied index group 8 'SideChain' 72: Merged two groups with AND: 5 13 -> 0 72: Group is empty 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 72: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 72: Going to read 1 old index file(s) 72: Deducing 6 atoms in the system from indices in the index file 72: 72: 0 System : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Removed group 0 'System' 72: 72: > 72: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 72: [ RUN ] GmxMakeNdx.Splitres 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into residues 72: 72: > 72: [ OK ] GmxMakeNdx.Splitres (1 ms) 72: [ RUN ] GmxMakeNdx.Splitat 72: 72: Reading structure file 72: Going to read 0 old index file(s) 72: Analysing residue names: 72: There are: 2 Water residues 72: 72: 0 System : 6 atoms 72: 1 Water : 6 atoms 72: 2 SOL : 6 atoms 72: 72: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 72: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 72: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 72: 'r': residue 'res' nr 'chain' char 72: "name": group 'case': case sensitive 'q': save and quit 72: 'ri': residue index 72: 72: > 72: Splitting group 1 'Water' into atoms 72: 72: > 72: [ OK ] GmxMakeNdx.Splitat (2 ms) 72: [----------] 7 tests from GmxMakeNdx (16 ms total) 72: 72: [----------] 4 tests from ReportMethodsTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Setting the LD random seed to -12845249 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 72: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 72: [ RUN ] ReportMethodsTest.WritesCorrectInformation 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 72: [ RUN ] ReportMethodsTest.ToolEndToEndTest 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: section: Methods 72: subsection: Simulation system 72: A system of 1 molecules (156 atoms) was simulated. 72: 72: subsection: Simulation settings 72: A total of 0 ns were simulated with a time step of 1 fs. 72: Neighbor searching was performed every 10 steps. 72: The Cut-off algorithm was used for electrostatic interactions. 72: with a cut-off of 1 nm. 72: A single cut-off of 1.1 nm was used for Van der Waals interactions. 72: [ OK ] ReportMethodsTest.ToolEndToEndTest (10 ms) 72: [----------] 4 tests from ReportMethodsTest (10 ms total) 72: 72: [----------] 4 tests from ConvertTprTest 72: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Setting the LD random seed to -68706648 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: Extending remaining runtime by 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 200000 72: Runtime for the run 200 ps 72: Run end step 200000 72: Run end time 200 ps 72: 72: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (636 ms) 72: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Setting the LD random seed to -598186 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: Extending remaining runtime to 100 ps 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 100000 72: Runtime for the run 100 ps 72: Run end step 100000 72: Run end time 100 ps 72: 72: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (389 ms) 72: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Setting nsteps to 102 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Setting the LD random seed to -1644192014 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Input file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 0 72: Runtime for the run 0 ps 72: Run end step 0 72: Run end time 0 ps 72: 72: 72: Output file: 72: Run start step 0 72: Run start time 0 ps 72: Step to be made during run 102 72: Runtime for the run 0.102 ps 72: Run end step 102 72: Run end time 0.102 ps 72: 72: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (470 ms) 72: [ RUN ] ConvertTprTest.generateVelocitiesTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Setting the LD random seed to 1836045687 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprTest.generateVelocitiesTest (307 ms) 72: [----------] 4 tests from ConvertTprTest (1803 ms total) 72: 72: [----------] 1 test from ConvertTprNoVelocityTest 72: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: 72: NOTE 3 [file lysozyme.top, line 1465]: 72: Zero-step energy minimization will alter the coordinates before 72: calculating the energy. If you just want the energy of a single point, 72: try zero-step MD (with unconstrained_start = yes). To do multiple 72: single-point energy evaluations of different configurations of the same 72: topology, use mdrun -rerun. 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 72: Setting the LD random seed to 2063119087 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (420 ms) 72: [----------] 1 test from ConvertTprNoVelocityTest (3215 ms total) 72: 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: trr version: GMX_trn_file (single precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (13 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:86: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (4 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 72: Will write trr: Trajectory in portable xdr format 72: Group 0 ( System) has 6 elements 72: Group 1 (FirstWaterMolecule) has 3 elements 72: Group 2 (SecondWaterMolecule) has 3 elements 72: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 72: -> frame 1 time 1.000 72: Last written: frame 1 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: Select group for output 72: Selected 2: 'SecondWaterMolecule' 72: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 72: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: ./src/gromacs/tools/tests/trjconv.cpp:123: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md (0 ms) 72: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats (24 ms total) 72: 72: [----------] 35 tests from Works/TrjconvDumpTest 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (3 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 72: Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (8 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 72: Precision of /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 72: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 72: Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 0 ps 72: -> frame 0 time 0.000 72: Last written: frame 0 time 0.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 72: Will write trr: Trajectory in portable xdr format 72: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 72: 72: Dumping frame at t= 1 ps 72: -> frame 0 time 1.000 72: Last written: frame 0 time 1.000 72: 72: 72: Note that major changes are planned in future for trjconv, to improve usability and utility. 72: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 (0 ms) 72: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 72: Cannot test H5MD reading if H5MD support is not configured 72: 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 (0 ms) 72: [----------] 35 tests from Works/TrjconvDumpTest (22 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 70 tests from 8 test suites ran. (6094 ms total) 72: [ PASSED ] 63 tests. 72: [ SKIPPED ] 7 tests, listed below: 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 72: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 72/104 Test #72: ToolUnitTests ............................. Passed 6.13 sec test 73 Start 73: ToolWithLeaksUnitTests 73: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests 73: Test timeout computed to be: 1920 73: [==========] Running 2 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 1 test from ConvertTprTest 73: [ RUN ] ConvertTprTest.selectIndexTest 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2026.3-Debian_1 (double precision) 73: Setting the LD random seed to 1610001150 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprTest.selectIndexTest (608 ms) 73: [----------] 1 test from ConvertTprTest (609 ms total) 73: 73: [----------] 1 test from ConvertTprNoVelocityTest 73: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 2 [file lysozyme.top, line 1465]: 73: System has non-zero total charge: 2.000000 73: Total charge should normally be an integer. See 73: https://manual.gromacs.org/current/user-guide/floating-point.html 73: for discussion on how close it should be to an integer. 73: 73: 73: 73: 73: NOTE 3 [file lysozyme.top, line 1465]: 73: Zero-step energy minimization will alter the coordinates before 73: calculating the energy. If you just want the energy of a single point, 73: try zero-step MD (with unconstrained_start = yes). To do multiple 73: single-point energy evaluations of different configurations of the same 73: topology, use mdrun -rerun. 73: 73: Number of degrees of freedom in T-Coupling group rest is 465.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.3-Debian_1 (double precision) 73: Group 0 ( System) has 156 elements 73: Group 1 ( Protein) has 156 elements 73: Group 2 ( Protein-H) has 75 elements 73: Group 3 ( C-alpha) has 10 elements 73: Group 4 ( Backbone) has 30 elements 73: Group 5 ( MainChain) has 40 elements 73: Group 6 ( MainChain+Cb) has 49 elements 73: Group 7 ( MainChain+H) has 52 elements 73: Group 8 ( SideChain) has 104 elements 73: Group 9 ( SideChain-H) has 35 elements 73: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 73: Reduced ilist BONDS from 156 to 75 entries 73: Reduced ilist ANGLES from 281 to 98 entries 73: Reduced ilist PDIHS from 29 to 12 entries 73: Reduced ilist RBDIHS from 313 to 89 entries 73: Reduced ilist LJ14 from 399 to 107 entries 73: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 73: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2026.3-Debian_1 (double precision) 73: Setting the LD random seed to -42502791 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 73: Analysing residue names: 73: There are: 10 Protein residues 73: Analysing Protein... 73: 73: This run will generate roughly 0 Mb of data 73: Selected 2: 'Protein-H' 73: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (609 ms) 73: [----------] 1 test from ConvertTprNoVelocityTest (610 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 2 tests from 2 test suites ran. (1220 ms total) 73: [ PASSED ] 2 tests. 73/104 Test #73: ToolWithLeaksUnitTests .................... Passed 1.26 sec test 74 Start 74: H5mdTests 74: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/h5md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/H5mdTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/h5md/tests 74: Test timeout computed to be: 60 74: [==========] Running 1 test from 1 test suite. 74: [----------] Global test environment set-up. 74: [----------] 1 test from H5mdDisabledTest 74: [ RUN ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled 74: [ OK ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled (0 ms) 74: [----------] 1 test from H5mdDisabledTest (0 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 1 test from 1 test suite ran. (0 ms total) 74: [ PASSED ] 1 test. 74/104 Test #74: H5mdTests ................................. Passed 0.03 sec test 75 Start 75: FileIOTests 75: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/FileIOTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/fileio/tests 75: Test timeout computed to be: 60 75: [==========] Running 432 tests from 17 test suites. 75: [----------] Global test environment set-up. 75: [----------] 4 tests from Checkpoint 75: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 75: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 75: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 75: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripInt64 75: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 75: [ RUN ] Checkpoint.KvtRoundTripReal 75: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 75: [----------] 4 tests from Checkpoint (0 ms total) 75: 75: [----------] 1 test from StructureIOTest 75: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 75: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 75: [----------] 1 test from StructureIOTest (0 ms total) 75: 75: [----------] 2 tests from FileMD5Test 75: [ RUN ] FileMD5Test.CanComputeMD5 75: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 75: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 75: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 75: [----------] 2 tests from FileMD5Test (2 ms total) 75: 75: [----------] 4 tests from FileTypeTest 75: [ RUN ] FileTypeTest.CorrectValueForEmptyString 75: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForNoExtension 75: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 75: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 75: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 75: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 75: [----------] 4 tests from FileTypeTest (0 ms total) 75: 75: [----------] 4 tests from ColorMapTest 75: [ RUN ] ColorMapTest.CanReadFromFile 75: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 75: [ RUN ] ColorMapTest.CanWriteToFile 75: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 75: [ RUN ] ColorMapTest.RoundTrip 75: [ OK ] ColorMapTest.RoundTrip (0 ms) 75: [ RUN ] ColorMapTest.SearchWorks 75: [ OK ] ColorMapTest.SearchWorks (0 ms) 75: [----------] 4 tests from ColorMapTest (0 ms total) 75: 75: [----------] 4 tests from MatioTest 75: [ RUN ] MatioTest.CanWriteToFile 75: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 75: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanConvertToNewRealMatrix 75: Converted a 4x3 matrix with 4 levels to reals 75: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 75: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 75: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (2 ms) 75: [----------] 4 tests from MatioTest (2 ms total) 75: 75: [----------] 3 tests from MrcSerializer 75: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 75: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 75: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 75: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 75: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 75: [----------] 3 tests from MrcSerializer (0 ms total) 75: 75: [----------] 4 tests from MrcDensityMap 75: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 75: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 75: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 75: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 75: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 75: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 75: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 75: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (8 ms) 75: [----------] 4 tests from MrcDensityMap (9 ms total) 75: 75: [----------] 8 tests from MrcDensityMapHeaderTest 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 75: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 75: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 75: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 75: [ RUN ] MrcDensityMapHeaderTest.IsSane 75: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 75: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 75: 75: [----------] 10 tests from ReadTest 75: [ RUN ] ReadTest.get_eint_ReadsInteger 75: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_eint64_ReadsInteger 75: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 75: 75: ERROR 1 [file unknown]: 75: Right hand side '0.8' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 75: [ RUN ] ReadTest.get_eint64_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not an 75: integer value 75: 75: 75: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsInteger 75: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 75: [ RUN ] ReadTest.get_ereal_ReadsFloat 75: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 75: [ RUN ] ReadTest.get_ereal_WarnsAboutString 75: 75: ERROR 1 [file unknown]: 75: Right hand side 'hello' for parameter 'test' in parameter file is not a 75: real value 75: 75: 75: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 75: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 75: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 75: [----------] 10 tests from ReadTest (0 ms total) 75: 75: [----------] 3 tests from TimeControlTest 75: [ RUN ] TimeControlTest.UnSetHasNoValue 75: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 75: [ RUN ] TimeControlTest.CanSetValue 75: [ OK ] TimeControlTest.CanSetValue (0 ms) 75: [ RUN ] TimeControlTest.CanUnsetValueAgain 75: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 75: [----------] 3 tests from TimeControlTest (0 ms total) 75: 75: [----------] 1 test from TngTest 75: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 75: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 75: [----------] 1 test from TngTest (0 ms total) 75: 75: [----------] 4 tests from XvgioTest 75: [ RUN ] XvgioTest.readXvgIntWorks 75: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgRealWorks 75: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 75: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 75: [ RUN ] XvgioTest.readXvgDeprecatedWorks 75: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 75: [----------] 4 tests from XvgioTest (0 ms total) 75: 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 75: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 75: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 75: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 75: 75: [----------] 370 tests from FileTypeMatch/FileTypeTest 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 (0 ms) 75: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 75: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 (0 ms) 75: [----------] 370 tests from FileTypeMatch/FileTypeTest (1 ms total) 75: 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 (0 ms) 75: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 75: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 (0 ms) 75: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest (0 ms total) 75: 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (5 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 75: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 75: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 75: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (7 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 432 tests from 17 test suites ran. (26 ms total) 75: [ PASSED ] 432 tests. 75/104 Test #75: FileIOTests ............................... Passed 0.08 sec test 76 Start 76: SelectionUnitTests 76: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/gromacs/selection/tests 76: Test timeout computed to be: 60 76: [==========] Running 202 tests from 11 test suites. 76: [----------] Global test environment set-up. 76: [----------] 1 test from IndexGroupTest 76: [ RUN ] IndexGroupTest.RemovesDuplicates 76: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 76: [----------] 1 test from IndexGroupTest (0 ms total) 76: 76: [----------] 15 tests from IndexBlockTest 76: [ RUN ] IndexBlockTest.CreatesUnknownBlock 76: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms) 76: [ RUN ] IndexBlockTest.CreatesAtomBlock 76: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 76: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 76: [ RUN ] IndexBlockTest.CreatesSingleBlock 76: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 76: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 76: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 76: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 76: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 76: [----------] 15 tests from IndexBlockTest (15 ms total) 76: 76: [----------] 11 tests from IndexMapTest 76: [ RUN ] IndexMapTest.InitializesAtomBlock 76: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 76: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 76: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 76: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 76: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 76: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 76: [ RUN ] IndexMapTest.InitializesMoleculeBlock 76: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsSingleBlock 76: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocks 76: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 76: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 76: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 76: [ RUN ] IndexMapTest.HandlesMultipleRequests 76: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 76: [----------] 11 tests from IndexMapTest (17 ms total) 76: 76: [----------] 3 tests from IndexGroupsAndNamesTest 76: [ RUN ] IndexGroupsAndNamesTest.containsNames 76: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 76: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 76: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 76: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 76: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 76: 76: [----------] 15 tests from NeighborhoodSearchTest 76: [ RUN ] NeighborhoodSearchTest.SimpleSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSearch (17 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 76: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (17 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchBox 76: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 76: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (8 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 76: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 76: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 76: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 76: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (42 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 76: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 76: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 76: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 76: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 76: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 76: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 76: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 76: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 76: [----------] 15 tests from NeighborhoodSearchTest (112 ms total) 76: 76: [----------] 13 tests from PositionCalculationTest 76: [ RUN ] PositionCalculationTest.ComputesAtomPositions 76: [ OK ] PositionCalculationTest.ComputesAtomPositions (5 ms) 76: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 76: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 76: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 76: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 76: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 76: [ RUN ] PositionCalculationTest.ComputesPositionMask 76: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 76: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 76: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (3 ms) 76: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 76: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 76: [----------] 13 tests from PositionCalculationTest (22 ms total) 76: 76: [----------] 33 tests from SelectionCollectionTest 76: [ RUN ] SelectionCollectionTest.HandlesNoSelections 76: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 76: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 76: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 76: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 76: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 76: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 76: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 76: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 76: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 76: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 76: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 76: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 76: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 76: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 76: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 76: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 76: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 76: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 76: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 76: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 76: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 76: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 76: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 76: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 76: [----------] 33 tests from SelectionCollectionTest (13 ms total) 76: 76: [----------] 14 tests from SelectionCollectionInteractiveTest 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 76: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (5 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 76: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 76: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 76: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 76: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 76: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 76: [----------] 14 tests from SelectionCollectionInteractiveTest (23 ms total) 76: 76: [----------] 71 tests from SelectionCollectionDataTest 76: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 76: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 76: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResnr 76: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 76: [ OK ] SelectionCollectionDataTest.HandlesResIndex (4 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 76: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 76: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 76: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesChain 76: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMass 76: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCharge 76: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 76: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 76: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 76: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBeta 76: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesResname 76: [ OK ] SelectionCollectionDataTest.HandlesResname (4 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 76: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (2 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 76: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (5 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 76: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (4 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 76: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 76: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 76: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 76: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 76: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 76: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 76: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (2 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 76: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 76: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 76: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 76: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 76: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 76: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 76: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (2 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic 76: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 76: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 76: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 76: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 76: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 76: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 76: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 76: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 76: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms) 76: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 76: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (4 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (7 ms) 76: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 76: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 76: [----------] 71 tests from SelectionCollectionDataTest (173 ms total) 76: 76: [----------] 17 tests from SelectionOptionTest 76: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 76: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 76: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 76: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 76: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptySelections 76: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 76: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 76: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelections 76: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 76: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesAdjuster 76: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 76: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 76: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 76: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 76: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 76: [----------] 17 tests from SelectionOptionTest (2 ms total) 76: 76: [----------] 9 tests from SelectionFileOptionTest 76: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 76: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 76: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 76: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 76: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 76: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 76: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 76: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 76: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 202 tests from 11 test suites ran. (382 ms total) 76: [ PASSED ] 202 tests. 76/104 Test #76: SelectionUnitTests ........................ Passed 0.42 sec test 77 Start 77: MdrunOutputTests 77: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 12 tests from 5 test suites. 77: [----------] Global test environment set-up. 77: [----------] 1 test from MdrunTest 77: [ RUN ] MdrunTest.WritesHelp 77: [ OK ] MdrunTest.WritesHelp (15 ms) 77: [----------] 1 test from MdrunTest (16 ms total) 77: 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -67223665 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.023 0.012 199.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 14.751 1.627 5.857 0.001 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (32 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -824180737 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.046 0.023 199.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 7.500 3.200 11.519 0.001 77: Reading frame 0 time 0.000 77: # Atoms 6 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (28 ms) 77: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 9.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: NVE simulation: will use the initial temperature of 2573.591 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: Setting the LD random seed to -18157593 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.011 199.0 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 15.977 1.502 5.408 0.001 77: Reading frame 0 time 0.000 77: # Atoms 3 77: Reading frame 1 time 0.001 Last frame 1 time 0.001 77: 77: 77: Item #frames Timestep (ps) 77: Step 2 0.001 77: Time 2 0.001 77: Lambda 0 77: Coords 2 0.001 77: Velocities 0 77: Forces 0 77: Box 2 0.001 77: Checking file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 77: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (15 ms) 77: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (76 ms total) 77: 77: [----------] 2 tests from Argon12/OutputFiles 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.025 0.012 199.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 117.533 0.204 0.735 0.016 77: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (21 ms) 77: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 15 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.248 0.124 199.9 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 11.859 2.024 7.286 0.002 77: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (141 ms) 77: [----------] 2 tests from Argon12/OutputFiles (163 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/Trajectories 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -161483150 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.027 0.014 196.0 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 44.310 0.542 1.950 0.003 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (35 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -1010831809 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.032 0.016 199.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 37.368 0.642 2.312 0.003 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (35 ms) 77: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 6 steps, 0.0 ps. 77: Setting the LD random seed to -1630274605 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.165 0.083 199.9 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 7.328 3.275 11.790 0.001 77: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (107 ms) 77: [----------] 3 tests from MdrunCanWrite/Trajectories (179 ms total) 77: 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -52355 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.016 0.008 198.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 31.507 0.762 2.742 0.002 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (22 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 77: 77: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: The Berendsen barostat does not generate any strictly correct ensemble, 77: and should not be used for new production simulations (in our opinion). 77: We recommend using the C-rescale barostat instead. 77: 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: 77: There was 1 WARNING 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to 1677572087 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 24 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.077 0.038 199.7 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 6.750 3.556 12.801 0.000 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (59 ms) 77: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 77: Number of degrees of freedom in T-Coupling group System is 12.00 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There was 1 NOTE 77: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2026.3-Debian_1 (double precision) 77: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -805685769 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.051 0.025 199.4 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 10.176 2.358 8.490 0.001 77: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (48 ms) 77: [----------] 3 tests from MdrunCanWrite/NptTrajectories (130 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 12 tests from 5 test suites ran. (637 ms total) 77: [ PASSED ] 12 tests. 77/104 Test #77: MdrunOutputTests .......................... Passed 0.67 sec test 78 Start 78: MdrunModulesTests 78: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 15 tests from 3 test suites. 78: [----------] Global test environment set-up. 78: [----------] 9 tests from DensityFittingTest 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.85652608067156e+03 78: Maximum force = 4.50998690851897e+03 on atom 3 78: Norm of force = 1.68168494163492e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -8531780 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (16 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -9.82077921283928e+03 78: Maximum force = 7.39548334240075e+03 on atom 2 78: Norm of force = 2.78250777177324e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -24609 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (12 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (10 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Overriding nsteps with value passed on the command line: 4 steps 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 4 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 5 steps. 78: Potential Energy = -5.47393359520241e+03 78: Maximum force = 6.13219949575544e+03 on atom 2 78: Norm of force = 1.77021426574818e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -25318403 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (10 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (12 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -3.85652608067156e+03 78: Maximum force = 4.50998690851897e+03 on atom 3 78: Norm of force = 1.68168494163492e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1274502038 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (16 ms) 78: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = -2.71386626041483e+04 78: Maximum force = 6.78276506555709e+03 on atom 2 78: Norm of force = 1.96088641457984e+03 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1543502831 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (9 ms) 78: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 78: 78: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 78: Setting the LD random seed to 1606319582 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 78: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (14 ms) 78: [ RUN ] DensityFittingTest.CheckpointWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (2) 78: 78: Number of degrees of freedom in T-Coupling group rest is 33.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -823477065 78: 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 19.650 1.221 4.397 0.003 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 78: Can not increase nstlist because an NVE ensemble is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.009 0.005 197.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 94.896 0.253 0.910 0.013 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (39 ms) 78: [----------] 9 tests from DensityFittingTest (143 ms total) 78: 78: [----------] 4 tests from MimicTest 78: [ RUN ] MimicTest.OneQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 19 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 182.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 439.258 0.055 0.197 0.061 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -12583057 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.OneQuantumMol (17 ms) 78: [ RUN ] MimicTest.AllQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 19 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 182.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 441.936 0.054 0.196 0.061 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -341606473 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.AllQuantumMol (13 ms) 78: [ RUN ] MimicTest.TwoQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 58 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.010 0.005 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.046 1.408 5.069 0.002 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -67543091 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.TwoQuantumMol (27 ms) 78: [ RUN ] MimicTest.BondCuts 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 66.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: NVE simulation: will use the initial temperature of 300.368 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 78: 78: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 71 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.010 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 8.952 2.681 9.651 0.002 78: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -25264705 78: 78: Generated 2211 of the 2211 non-bonded parameter combinations 78: 78: Generated 2211 of the 2211 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] MimicTest.BondCuts (38 ms) 78: [----------] 4 tests from MimicTest (97 ms total) 78: 78: [----------] 2 tests from WithIntegrator/ImdTest 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 78: Generating 1-4 interactions: fudge = 1 78: 78: NOTE 1 [file glycine_vacuo.top, line 12]: 78: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 78: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 78: the time step of 2.0e-03 ps. 78: Maybe you forgot to change the constraints mdp option. 78: 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 53661. 78: IMD: -imdwait not set, starting simulation. 78: starting mdrun 'Glycine' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -811597830 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: NOTE: 18 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.100 0.050 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 10.375 2.313 16.655 0.001 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (184 ms) 78: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 78: apply to steep. 78: 78: Generating 1-4 interactions: fudge = 1 78: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 78: Number of degrees of freedom in T-Coupling group System is 27.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2026.3-Debian_1 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: IMD: Enabled. This simulation will accept incoming IMD connections. 78: IMD: Pulling from IMD remote is enabled (-imdpull). 78: IMD: Setting port for connection requests to 0. 78: IMD: Setting up incoming socket. 78: IMD: Listening for IMD connection on port 37301. 78: IMD: -imdwait not set, starting simulation. 78: 78: Steepest Descents: 78: Tolerance (Fmax) = 1.00000e+01 78: Number of steps = 2 78: 78: Energy minimization reached the maximum number of steps before the forces 78: reached the requested precision Fmax < 10. 78: 78: writing lowest energy coordinates. 78: 78: Steepest Descents did not converge to Fmax < 10 in 3 steps. 78: Potential Energy = 1.19770464690297e+03 78: Maximum force = 1.77948604657896e+04 on atom 9 78: Norm of force = 7.87328617833980e+03 78: Setting the LD random seed to -553713937 78: 78: Generated 20503 of the 20503 non-bonded parameter combinations 78: 78: Generated 17396 of the 20503 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Glycine' 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (117 ms) 78: [----------] 2 tests from WithIntegrator/ImdTest (301 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 15 tests from 3 test suites ran. (599 ms total) 78: [ PASSED ] 15 tests. 78/104 Test #78: MdrunModulesTests ......................... Passed 0.63 sec test 79 Start 79: MdrunIOTests 79: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 76 tests from 13 test suites. 79: [----------] Global test environment set-up. 79: [----------] 9 tests from GromppTest 79: [ RUN ] GromppTest.EmptyMdpFileWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -149554 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.EmptyMdpFileWorks (7 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group rest: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to 1794913783 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorks (7 ms) 79: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Simulated annealing for group Methanol: Single, 3 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 3.0 280.0 79: 6.0- 270.0 79: Simulated annealing for group SOL: Periodic, 4 timepoints 79: Time (ps) Temperature (K) 79: 0.0 298.0 79: 2.0 320.0 79: 4.0 320.0 79: 6.0 298.0 79: Number of degrees of freedom in T-Coupling group Methanol is 7.20 79: Number of degrees of freedom in T-Coupling group SOL is 4.80 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -270533253 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (7 ms) 79: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 79: Setting the LD random seed to -134217802 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (26 ms) 79: [ RUN ] GromppTest.HandlesMaxwarn 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: The Berendsen thermostat does not generate the correct kinetic energy 79: distribution, and should not be used for new production simulations (in 79: our opinion). We would recommend the V-rescale thermostat. 79: 79: Number of degrees of freedom in T-Coupling group System is 12.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Setting the LD random seed to -9443873 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.HandlesMaxwarn (3 ms) 79: [ RUN ] GromppTest.MaxwarnShouldBePositive 79: [ OK ] GromppTest.MaxwarnShouldBePositive (5 ms) 79: [ RUN ] GromppTest.ValidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: 0.613 nm 0.000 nm 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -218245770 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] GromppTest.ValidTransformationCoord (5 ms) 79: [ RUN ] GromppTest.InvalidTransformationCoord 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Pull group 1 'SOL' has 3 atoms 79: Pull group 2 'Methanol' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 5 79: 2 3 2 0.613 nm 0.000 nm 79: Setting the LD random seed to 2075119583 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) 79: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 79: Setting the LD random seed to 1936713718 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (14 ms) 79: [----------] 9 tests from GromppTest (83 ms total) 79: 79: [----------] 6 tests from MdrunTerminationTest 79: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -268909527 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 28 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.068 0.034 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.651 3.137 11.293 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 23 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.055 0.027 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.443 2.541 9.149 0.001 79: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (88 ms) 79: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 1, rlist from 1.035 to 1 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 79: Setting the LD random seed to 1440605694 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE: 19 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.062 0.031 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 5.604 4.282 15.417 0.000 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 102 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 100 79: Runtime for the run 0.1 ps 79: Run end step 100 79: Run end time 0.1 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 102 79: Runtime for the run 0.102 ps 79: Run end step 102 79: Run end time 0.102 ps 79: 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.736 0.368 200.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 23.934 1.003 3.610 0.002 79: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (427 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -274760611 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 19 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.015 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 17.010 1.411 5.079 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 24 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.053 0.027 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.723 2.468 8.886 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 6 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.044 0.022 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.808 2.032 7.317 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 8 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 6 79: Runtime for the run 0.006 ps 79: Run end step 6 79: Run end time 0.006 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 8 79: Runtime for the run 0.008 ps 79: Run end step 8 79: Run end time 0.008 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.045 0.023 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.450 2.096 7.546 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: NOTE: 68 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.013 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.773 3.543 12.757 0.000 79: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (164 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -283336705 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.020 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 12.845 1.868 6.727 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 20 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.085 0.042 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.198 2.353 8.472 0.001 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (88 ms) 79: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -226508817 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 20 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.064 0.032 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 8.110 2.959 10.654 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 4 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (49 ms) 79: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -1115701415 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.067 0.034 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.730 3.105 11.177 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Setting nsteps to 4 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: Input file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 2 79: Runtime for the run 0.002 ps 79: Run end step 2 79: Run end time 0.002 ps 79: 79: 79: Output file: 79: Run start step 0 79: Run start time 0 ps 79: Step to be made during run 4 79: Runtime for the run 0.004 ps 79: Run end step 4 79: Run end time 0.004 ps 79: 79: 79: Writing final coordinates. 79: 79: NOTE: 28 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.062 0.031 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 8.285 2.897 10.428 0.001 79: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (91 ms) 79: [----------] 6 tests from MdrunTerminationTest (909 ms total) 79: 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 130.951 0.183 0.660 0.009 79: trr version: GMX_trn_file (double precision) 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: Will write trr: Trajectory in portable xdr format 79: Last frame -1 time 0.016 79: 79: Dumping frame at t= 0.016 ps 79: -> frame 0 time 0.016 79: Last written: frame 0 time 0.016 79: 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Last frame -1 time 0.016 79: 79: There were 3 NOTEs 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Note that major changes are planned in future for trjconv, to improve usability and utility. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: Analysing residue names: 79: There are: 2 Water residues 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: Reading Coordinates, Velocities and Box size from old trajectory 79: 79: Will read whole trajectory 79: 79: Using frame at t = 0.016 ps 79: 79: Starting time for run is 0 ps 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (20 ms) 79: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 179.332 0.134 0.482 0.012 79: 79: 79: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (29 ms) 79: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (51 ms total) 79: 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 177.790 0.135 0.486 0.025 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.011 122.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 73.341 0.327 1.178 0.010 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 156.584 0.153 0.552 0.022 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (51 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 185.913 0.129 0.465 0.026 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.736 0.313 1.126 0.011 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 79.745 0.301 1.083 0.011 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (48 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.268 0.134 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.951 2.192 7.890 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.146 0.073 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.627 2.258 8.130 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.153 0.077 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.137 2.368 8.524 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (321 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.145 0.072 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 20.287 1.183 4.259 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.005 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 163.787 0.147 0.528 0.023 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 10 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.058 0.029 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 26.739 0.898 3.231 0.004 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (128 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.185 0.093 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 15.856 1.514 5.449 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.064 0.032 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 24.328 0.987 3.551 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 68.981 0.348 1.253 0.010 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (181 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.113 0.056 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 26.026 0.922 3.320 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.124 0.062 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 12.524 1.916 6.899 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 19 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.064 0.032 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 24.196 0.992 3.571 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (193 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.013 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 116.413 0.206 0.742 0.016 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.159 0.079 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.795 2.450 8.821 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 24 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.136 0.068 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.407 2.104 7.574 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (191 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.146 0.073 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 20.114 1.193 4.295 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.049 0.024 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 31.845 0.754 2.713 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.287 0.315 1.133 0.011 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (135 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.212 0.106 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 13.850 1.733 6.238 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.088 0.044 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 17.606 1.363 4.907 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.020 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 39.737 0.604 2.174 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (210 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.185 0.093 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 15.868 1.512 5.445 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 80.764 0.297 1.070 0.006 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 87.946 0.273 0.982 0.006 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (142 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.242 0.121 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 12.119 1.980 7.129 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 73.247 0.328 1.180 0.005 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.196 0.098 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.916 3.032 10.915 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (260 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 10 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.276 0.138 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.638 2.256 8.122 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.223 0.112 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.961 3.448 12.413 0.000 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.135 0.068 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.470 2.092 7.533 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (355 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.018 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 83.611 0.287 1.033 0.006 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 65.107 0.369 1.327 0.005 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.020 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 38.678 0.621 2.234 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (79 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.237 0.119 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 12.380 1.939 6.979 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.147 0.073 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.581 2.268 8.165 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 147.080 0.163 0.587 0.010 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (249 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.014 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 107.920 0.222 0.801 0.007 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 196.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 154.536 0.155 0.559 0.011 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.010 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 75.217 0.319 1.149 0.005 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (56 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.008 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 176.138 0.136 0.491 0.012 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.162 0.081 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.616 2.496 8.985 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.159 0.080 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.768 2.457 8.845 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (215 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.384 0.192 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.654 3.135 11.287 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.291 0.146 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 5.342 4.493 16.174 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.041 0.021 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 37.411 0.642 2.310 0.013 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (428 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 181.050 0.133 0.477 0.061 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.041 0.021 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 37.723 0.636 2.290 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.005 198.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 141.539 0.170 0.610 0.048 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (103 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.045 0.023 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 64.946 0.370 1.330 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.019 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 41.027 0.585 2.106 0.014 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.075 0.037 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 20.741 1.157 4.166 0.007 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (132 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: NVE simulation: will use the initial temperature of 456.887 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.516 0.258 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 5.692 4.216 15.178 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 65.921 0.364 1.311 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.071 0.036 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 21.870 1.097 3.951 0.007 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (369 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.419 0.209 200.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.015 3.421 12.317 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.239 0.120 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.498 3.694 13.297 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 101.207 0.237 0.854 0.034 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (465 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.442 0.221 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.647 3.611 12.999 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.284 0.142 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 5.483 4.377 15.758 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.245 0.123 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.333 3.790 13.643 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (744 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.831 0.416 200.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 3.533 6.793 24.453 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.073 0.037 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 21.121 1.136 4.091 0.007 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 73.312 0.327 1.179 0.025 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (640 ms) 79: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file unknown]: 79: You are using constraints on all bonds, whereas the forcefield has been 79: parametrized only with constraints involving hydrogen atoms. We suggest 79: using constraints = h-bonds instead, this will also improve performance. 79: 79: Number of degrees of freedom in T-Coupling group System is 23.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: There are 9 non-linear virtual site constructions. Their contribution to 79: the energy error is approximated. In most cases this does not affect the 79: error significantly. 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 79: 79: Cleaning up constraints and constant bonded interactions with virtual sites 79: 79: Removed 18 Angles with virtual sites, 21 left 79: 79: Removed 10 Proper Dih.s with virtual sites, 44 left 79: 79: Converted 15 Constraints with virtual sites to connections, 7 left 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.018 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 81.218 0.296 1.064 0.027 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.337 0.168 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 4.615 5.200 18.721 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 79: 79: Update groups can not be used for this system because an incompatible virtual site type is used 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine dipeptide in vacuo' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.018 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 42.967 0.559 2.011 0.014 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (362 ms) 79: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (6066 ms total) 79: 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.386 0.193 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.614 3.152 11.347 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.153 0.077 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.160 2.362 8.504 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 84.851 0.283 1.018 0.035 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (354 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.050 0.025 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 58.226 0.412 1.484 0.024 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 17 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.161 0.081 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.632 2.492 8.970 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.166 0.083 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.374 2.560 9.217 0.004 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (260 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.367 0.184 200.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.997 3.001 10.804 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 71.953 0.334 1.201 0.030 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 70.936 0.338 1.218 0.030 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (267 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 294.908 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.163 0.082 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 18.017 1.332 4.795 0.008 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.220 0.110 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.043 3.408 12.268 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.202 0.101 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.694 3.119 11.230 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (367 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.127 0.064 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 23.023 1.042 3.753 0.010 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.204 0.102 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.604 3.156 11.363 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.119 0.059 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 13.070 1.836 6.611 0.005 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (354 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.203 0.102 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 14.445 1.661 5.981 0.006 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.224 0.112 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 6.933 3.462 12.462 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.158 0.079 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.859 2.434 8.763 0.004 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (521 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.056 0.028 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 52.107 0.461 1.658 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.163 0.082 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.477 2.532 9.117 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.010 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 78.931 0.304 1.095 0.033 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (248 ms) 79: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.151 0.076 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.398 1.237 4.454 0.008 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.178 0.091 195.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 8.533 2.813 10.125 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.044 0.022 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 35.063 0.684 2.464 0.015 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (299 ms) 79: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2679 ms total) 79: 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.008 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 179.934 0.133 0.480 0.025 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 64.199 0.374 1.346 0.009 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.017 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 46.987 0.511 1.839 0.007 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (79 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 291.143 0.082 0.297 0.040 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.013 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 58.175 0.413 1.485 0.008 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.110 0.055 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 14.067 1.706 6.142 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (113 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.096 0.048 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 30.461 0.788 2.836 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.125 0.062 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 12.458 1.926 6.935 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 19 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.131 0.065 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.900 2.017 7.261 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (215 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 44 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.016 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 91.033 0.264 0.949 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.116 0.058 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 13.341 1.799 6.476 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.122 0.061 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 12.726 1.886 6.789 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (188 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.051 0.026 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 57.335 0.419 1.507 0.008 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.215 0.107 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.235 3.317 11.941 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.081 0.041 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.115 1.256 4.520 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (221 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.067 0.034 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 43.623 0.550 1.981 0.006 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.096 0.048 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 16.174 1.484 5.342 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.120 0.060 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 12.915 1.858 6.690 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (178 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.042 0.021 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 69.819 0.344 1.237 0.010 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.047 0.023 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 33.090 0.725 2.611 0.005 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 42 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.016 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 49.659 0.483 1.740 0.007 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (80 ms) 79: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.076 0.038 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 38.515 0.623 2.243 0.005 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.153 0.076 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 10.177 2.358 8.490 0.001 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.057 0.029 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 27.169 0.883 3.180 0.004 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (178 ms) 79: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1256 ms total) 79: 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.009 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 157.980 0.152 0.547 0.022 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 196.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 154.324 0.156 0.560 0.021 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.017 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 45.347 0.529 1.905 0.006 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (45 ms) 79: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.261 0.131 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.237 2.136 7.689 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.141 0.070 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.050 2.172 7.819 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.131 0.066 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.850 2.025 7.291 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (301 ms) 79: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (347 ms total) 79: 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.155 0.078 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 18.920 1.269 4.567 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.019 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 40.659 0.590 2.125 0.006 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.005 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 149.988 0.160 0.576 0.021 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (128 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 153.543 0.156 0.563 0.021 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 197.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 104.942 0.229 0.823 0.015 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.010 115.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 74.740 0.321 1.156 0.010 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (48 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.007 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 198.058 0.121 0.436 0.028 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 64.362 0.373 1.342 0.009 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 69.340 0.346 1.246 0.010 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (57 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.017 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 88.592 0.271 0.975 0.012 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 17 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.135 0.068 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 11.504 2.086 7.510 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.050 0.025 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 30.753 0.780 2.809 0.004 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (156 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 24 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.055 0.027 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 53.570 0.448 1.613 0.007 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.079 0.040 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.640 1.222 4.399 0.003 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.104 0.052 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 14.893 1.611 5.801 0.002 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (152 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.226 0.113 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 13.008 1.845 6.642 0.002 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.013 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 62.182 0.386 1.389 0.009 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.008 198.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 102.656 0.234 0.842 0.014 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (159 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 79: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 79: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.014 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 105.455 0.228 0.819 0.015 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.007 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 111.967 0.214 0.772 0.016 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 23 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.011 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 69.552 0.345 1.242 0.010 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (65 ms) 79: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (769 ms total) 79: 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 79: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: MTTK coupling is deprecated and will soon be removed 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.018 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 81.656 0.294 1.058 0.011 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.018 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 43.243 0.555 1.998 0.006 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.006 197.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 129.687 0.185 0.666 0.018 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (71 ms) 79: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (71 ms total) 79: 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.014 198.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 106.649 0.225 0.810 0.007 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.015 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 53.401 0.449 1.618 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.013 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 61.277 0.392 1.410 0.004 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (64 ms) 79: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 2573.591 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.048 0.024 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 60.554 0.396 1.427 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.014 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 55.098 0.436 1.568 0.004 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.012 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 62.229 0.386 1.388 0.004 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (76 ms) 79: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (141 ms total) 79: 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Setting the AWH bias MC random seed to 2029906670 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -1081157633 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.009 197.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 166.552 0.144 0.519 0.042 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.051 0.025 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 30.567 0.785 2.827 0.008 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 65.547 0.366 1.318 0.017 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (119 ms) 79: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 79: Setting the AWH bias MC random seed to -1241514582 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Setting the AWH bias MC random seed to -570732611 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 119.080 0.202 0.726 0.030 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.016 197.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 47.317 0.507 1.826 0.012 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.017 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 46.422 0.517 1.861 0.012 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (101 ms) 79: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (221 ms total) 79: 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 79: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 79.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There was 1 NOTE 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps. 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generated 2485 of the 2485 non-bonded parameter combinations 79: 79: Generated 2485 of the 2485 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'nonanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.014 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 103.068 0.233 0.838 0.043 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 8 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 25 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.049 0.025 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 31.643 0.758 2.731 0.013 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun '30 atom system in water' 79: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.198 0.099 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.835 3.063 11.027 0.003 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (216 ms) 79: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (217 ms total) 79: 79: [----------] 3 tests from Checking/InitialConstraintsTest 79: [ RUN ] Checking/InitialConstraintsTest.Works/0 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to 2004876726 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.043 0.022 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 7.933 3.025 10.891 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (34 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/1 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to -1124346945 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.065 0.032 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 5.323 4.509 16.231 0.000 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (42 ms) 79: [ RUN ] Checking/InitialConstraintsTest.Works/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: Integrator method md-vv-avek is implemented primarily for validation 79: purposes; for molecular dynamics, you should probably be using md or 79: md-vv 79: 79: Number of degrees of freedom in T-Coupling group rest is 11.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 1141.954 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2026.3-Debian_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 1 steps, 0.0 ps. 79: Setting the LD random seed to -1879056777 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: turning H bonds into constraints... 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.020 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 8.641 2.777 9.998 0.001 79: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (37 ms) 79: [----------] 3 tests from Checking/InitialConstraintsTest (115 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 76 tests from 13 test suites ran. (13112 ms total) 79: [ PASSED ] 76 tests. 79/104 Test #79: MdrunIOTests .............................. Passed 13.15 sec test 80 Start 80: MdrunTestsOneRank 80: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 31 tests from 9 test suites. 80: [----------] Global test environment set-up. 80: [----------] 2 tests from AwhTest 80: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.234 0.117 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 15.490 1.549 5.578 0.004 80: [ OK ] AwhTest.SingleBiasMultiDimCanRun (162 ms) 80: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.268 0.134 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 13.548 1.772 6.377 0.003 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 198.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 106.108 0.226 0.814 0.027 80: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (186 ms) 80: [----------] 2 tests from AwhTest (349 ms total) 80: 80: [----------] 1 test from CompelTest 80: [ RUN ] CompelTest.SwapCanRun 80: Generating 1-4 interactions: fudge = 0.5 80: Split0 group 'Ch0' contains 83 atoms. 80: Split1 group 'Ch1' contains 83 atoms. 80: Solvent group 'SOL' contains 11931 atoms. 80: Swap group 'NA+' contains 19 atoms. 80: Swap group 'CL-' contains 19 atoms. 80: Number of degrees of freedom in T-Coupling group System is 27869.00 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Determining initial numbers of ions per compartment. 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 2 steps, 0.0 ps. 80: Setting the LD random seed to -1074529281 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning all bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.544 0.272 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 3.810 6.299 90.711 0.152 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 80: 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Copying channel fluxes from checkpoint file data 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: NOTE: 15 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.429 0.215 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 4.828 4.971 71.583 0.193 80: [ OK ] CompelTest.SwapCanRun (1229 ms) 80: [----------] 1 test from CompelTest (1229 ms total) 80: 80: [----------] 6 tests from BondedInteractionsTest 80: [ RUN ] BondedInteractionsTest.NormalBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 19 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 185.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 447.392 0.054 0.193 0.021 80: Setting the LD random seed to -1355651089 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalBondWorks (12 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 17 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 185.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 419.430 0.057 0.206 0.019 80: Setting the LD random seed to 937614717 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedBondWorks (18 ms) 80: [ RUN ] BondedInteractionsTest.NormalAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 17 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.000 0.000 186.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 409.941 0.059 0.211 0.019 80: Setting the LD random seed to -1210069091 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalAngleWorks (8 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 54 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.012 0.006 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 14.709 1.632 5.874 0.001 80: Setting the LD random seed to -2030050882 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (23 ms) 80: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 47 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.012 0.006 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 14.943 1.606 5.782 0.001 80: Setting the LD random seed to 2078277535 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalDihedralWorks (23 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 23 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.012 199.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 6.918 3.469 12.490 0.000 80: Setting the LD random seed to -33700370 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (28 ms) 80: [----------] 6 tests from BondedInteractionsTest (115 ms total) 80: 80: [----------] 2 tests from BoxDeformationTest 80: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 41 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 198.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 24.237 0.990 7.130 0.002 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -57418772 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Setting gen_seed to -134365190 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (20 ms) 80: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group rest is 1293.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 20 steps, 0.0 ps. 80: Setting the LD random seed to -311889 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 80: 80: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 80: 80: Estimate for the relative computational load of the PME mesh part: 0.18 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.417 0.209 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 17.391 1.380 9.936 0.065 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (617 ms) 80: [----------] 2 tests from BoxDeformationTest (638 ms total) 80: 80: [----------] 1 test from PositionRestraintCommTest 80: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any of the VCM groups 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any center of mass motion removal group. 80: This may lead to artifacts. 80: In most cases one should use one group for the whole system. 80: 80: Number of degrees of freedom in T-Coupling group System is 29527.73 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Channel_coco in octane membrane' 80: 10 steps, 0.0 ps. 80: Setting the LD random seed to 1591656414 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 14 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.814 0.407 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 4.668 5.142 37.021 0.373 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (848 ms) 80: [----------] 1 test from PositionRestraintCommTest (848 ms total) 80: 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -90255367 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.012 0.006 198.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 69.269 0.346 1.247 0.018 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1140953603 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.179 0.090 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 4.822 4.977 17.919 0.001 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 80: 80: 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (232 ms) 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1409295361 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 20 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.136 0.068 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 6.360 3.774 13.586 0.002 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1073942341 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.94 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 12 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.154 0.077 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 5.618 4.272 15.379 0.001 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (246 ms) 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (479 ms total) 80: 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -9732705 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.070 0.036 196.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 12.086 1.986 7.149 0.001 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1610595839 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.087 0.044 199.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 9.868 2.432 8.756 0.001 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (138 ms) 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (139 ms total) 80: 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 14 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.153 0.077 199.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 10.141 2.367 8.520 0.003 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (117 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 198.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 108.046 0.222 0.800 0.028 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (32 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 55.243 0.434 1.564 0.014 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (33 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.013 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 60.730 0.395 1.423 0.015 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (26 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.172 0.086 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 9.016 2.662 9.583 0.002 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (107 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 80: Parrinello-Rahman is not implemented in md-vv. 80: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.010 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 78.193 0.307 1.105 0.020 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (40 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.151 0.076 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 10.272 2.336 8.411 0.003 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (112 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.026 0.013 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 59.010 0.407 1.464 0.015 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (41 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.109 0.054 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 14.302 1.678 6.041 0.004 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (101 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.156 0.078 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 9.957 2.410 8.677 0.003 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (158 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.129 0.064 199.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 12.076 1.987 7.154 0.003 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (135 ms) 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest (907 ms total) 80: 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -25466401 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.016 199.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 99.402 0.241 1.738 0.003 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (27 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -67341345 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.009 0.005 197.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 334.993 0.072 0.516 0.012 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (18 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 1879045499 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 199.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 144.823 0.166 1.193 0.005 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (15 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -810355713 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.013 0.007 198.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 237.312 0.101 0.728 0.008 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (12 ms) 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (83 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 31 tests from 9 test suites ran. (4912 ms total) 80: [ PASSED ] 30 tests. 80: [ SKIPPED ] 1 test, listed below: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80/104 Test #80: MdrunTestsOneRank ......................... Passed 4.94 sec test 81 Start 81: MdrunTestsTwoRanks 81: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 31 tests from 9 test suites. 81: [----------] Global test environment set-up. 81: [----------] 2 tests from AwhTest 81: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 6.8%. 81: The balanceable part of the MD step is 55%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 3.8%. 81: 81: 81: NOTE: 22 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.845 0.211 399.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 8.581 2.797 10.069 0.002 81: [ OK ] AwhTest.SingleBiasMultiDimCanRun (847 ms) 81: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'C_&_r_1' has 1 atoms 81: Pull group 2 'N_&_r_2' has 1 atoms 81: Pull group 3 'CA' has 1 atoms 81: Pull group 4 'C_&_r_2' has 1 atoms 81: Pull group 5 'N_&_r_3' has 1 atoms 81: Number of degrees of freedom in T-Coupling group System is 51.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 1 0 81: 2 1 0 179.098 deg 0.000 deg 81: 2 1 0 81: 3 1 0 158.667 deg 0.000 deg 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 20 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 15.3%. 81: The balanceable part of the MD step is 52%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.0%. 81: 81: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.056 0.014 396.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 127.545 0.188 0.677 0.032 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 17.8%. 81: The balanceable part of the MD step is 48%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 8.5%. 81: 81: NOTE: 8.5 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.882 0.221 398.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 8.210 2.923 10.523 0.002 81: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (406 ms) 81: [----------] 2 tests from AwhTest (1254 ms total) 81: 81: [----------] 1 test from CompelTest 81: [ RUN ] CompelTest.SwapCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Split0 group 'Ch0' contains 83 atoms. 81: Split1 group 'Ch1' contains 83 atoms. 81: Solvent group 'SOL' contains 11931 atoms. 81: Swap group 'NA+' contains 19 atoms. 81: Swap group 'CL-' contains 19 atoms. 81: Number of degrees of freedom in T-Coupling group System is 27869.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Determining initial numbers of ions per compartment. 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 2 steps, 0.0 ps. 81: Setting the LD random seed to -2065 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: turning all bonds into constraints... 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: turning all bonds into constraints... 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning all bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.2%. 81: The balanceable part of the MD step is 19%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.2%. 81: 81: 81: NOTE: 30 % of the run time was spent in domain decomposition, 81: 19 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.056 0.264 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 3.923 6.117 88.087 0.157 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 81: 81: Update groups can not be used for this system because there are three or more consecutively coupled constraints 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: SWAP: Setting pointers for checkpoint writing 81: SWAP: Copying channel fluxes from checkpoint file data 81: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 81: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 81: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 81: starting mdrun 'Channel_coco in octane membrane' 81: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 81: 81: Writing final coordinates. 81: 81: NOTE: 14 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.743 0.186 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.580 4.301 61.931 0.223 81: [ OK ] CompelTest.SwapCanRun (1888 ms) 81: [----------] 1 test from CompelTest (1889 ms total) 81: 81: [----------] 6 tests from BondedInteractionsTest 81: [ RUN ] BondedInteractionsTest.NormalBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 45 % of the run time was spent in domain decomposition, 81: 32 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.100 0.025 399.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 3.457 6.943 24.996 0.000 81: Setting the LD random seed to -5260193 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalBondWorks (84 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 2 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 57 % of the run time was spent in domain decomposition, 81: 24 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.084 0.021 399.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.124 5.820 20.951 0.000 81: Setting the LD random seed to -1654686739 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedBondWorks (99 ms) 81: [ RUN ] BondedInteractionsTest.NormalAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 50 % of the run time was spent in domain decomposition, 81: 25 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.105 0.026 399.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 3.289 7.296 26.266 0.000 81: Setting the LD random seed to 2128066459 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalAngleWorks (91 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 41 % of the run time was spent in domain decomposition, 81: 17 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.066 0.017 399.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.227 4.591 16.528 0.000 81: Setting the LD random seed to -696582482 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (38 ms) 81: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 33 % of the run time was spent in domain decomposition, 81: 10 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.102 0.026 399.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 3.378 7.104 25.575 0.000 81: Setting the LD random seed to 2008792510 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.NormalDihedralWorks (49 ms) 81: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: 81: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 81: In moleculetype 'butane' 4 atoms are not bound by a potential or 81: constraint to any other atom in the same moleculetype. Although 81: technically this might not cause issues in a simulation, this often means 81: that the user forgot to add a bond/potential/constraint or put multiple 81: molecules in the same moleculetype definition by mistake. Run with -v to 81: get information for each atom. 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro' 81: 81: Reading frames from gro file 'A single butane', 4 atoms. 81: Reading frame 0 time 0.000 Last frame 0 time 0.000 81: 81: NOTE: 36 % of the run time was spent in domain decomposition, 81: 18 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.120 0.030 399.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 2.879 8.337 30.013 0.000 81: Setting the LD random seed to -33282 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'butane' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (63 ms) 81: [----------] 6 tests from BondedInteractionsTest (428 ms total) 81: 81: [----------] 2 tests from BoxDeformationTest 81: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 39 % of the run time was spent in domain decomposition, 81: 31 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.107 0.027 397.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 6.393 3.754 27.029 0.000 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -403702325 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Setting gen_seed to 1727227774 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (69 ms) 81: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group rest is 1293.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 20 steps, 0.0 ps. 81: Setting the LD random seed to -68158625 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 81: 81: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 81: 81: Estimate for the relative computational load of the PME mesh part: 0.18 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB got disabled because it was unsuitable to use. 81: Average load imbalance: 19.4%. 81: The balanceable part of the MD step is 15%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.9%. 81: 81: 81: NOTE: 15 % of the run time was spent in domain decomposition, 81: 5 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.911 0.478 399.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 7.593 3.161 22.757 0.028 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (820 ms) 81: [----------] 2 tests from BoxDeformationTest (889 ms total) 81: 81: [----------] 1 test from PositionRestraintCommTest 81: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (10) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any of the VCM groups 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: 13489 atoms are not part of any center of mass motion removal group. 81: This may lead to artifacts. 81: In most cases one should use one group for the whole system. 81: 81: Number of degrees of freedom in T-Coupling group System is 29527.73 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 81: Removing center of mass motion in the presence of position restraints 81: might cause artifacts. When you are using position restraints to 81: equilibrate a macro-molecule, the artifacts are usually negligible. 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Channel_coco in octane membrane' 81: 10 steps, 0.0 ps. 81: Setting the LD random seed to 1423137199 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 1 bonded neighbours molecule type 'NA' 81: 81: Excluding 1 bonded neighbours molecule type 'CL' 81: 81: Excluding 3 bonded neighbours molecule type 'Protein' 81: 81: Excluding 3 bonded neighbours molecule type 'OCT' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/OctaneSandwich.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: Chain0: 2.207 2.168 7.330 81: Chain1: 2.228 2.186 2.401 81: 81: This run will generate roughly 1 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.806 0.452 399.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.209 5.702 41.052 0.337 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1531 ms) 81: [----------] 1 test from PositionRestraintCommTest (1531 ms total) 81: 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to 518502780 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.051 0.013 397.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 33.460 0.717 2.582 0.009 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -293750857 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.424 0.106 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.072 5.894 21.220 0.001 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 81: 81: 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (853 ms) 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -67108906 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 45 % of the run time was spent in domain decomposition, 81: 7 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.604 0.151 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 2.858 8.398 30.232 0.001 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 3 [file ala.top, line 256]: 81: For energy conservation with LINCS, lincs_iter should be 2 or larger. 81: 81: 81: Number of degrees of freedom in T-Coupling group rest is 54.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'UNNAMED in water' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -33555652 81: 81: Generated 2211 of the 2211 non-bonded parameter combinations 81: 81: Generated 2211 of the 2211 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 81: 81: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 81: 81: Estimate for the relative computational load of the PME mesh part: 0.94 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 11 % of the run time was spent in domain decomposition, 81: 3 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.390 0.097 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.432 5.415 19.494 0.001 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (1091 ms) 81: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1944 ms total) 81: 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 81: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to 1607982442 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 21 % of the run time was spent in domain decomposition, 81: 8 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.272 0.068 399.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 6.342 3.784 13.623 0.000 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Pull group 1 'FirstWaterMolecule' has 3 atoms 81: Pull group 2 'SecondWaterMolecule' has 3 atoms 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Pull group natoms pbc atom distance at start reference at t=0 81: 1 3 2 81: 2 3 5 1.112 nm 1.000 nm 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 4 steps, 0.0 ps. 81: Setting the LD random seed to -1375834126 81: 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 12 % of the run time was spent in domain decomposition, 81: 5 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 17 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.222 0.056 399.3 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 7.772 3.088 11.117 0.001 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 81: 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (296 ms) 81: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (296 ms total) 81: 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 4.1%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.1%. 81: 81: 81: NOTE: 18 % of the run time was spent in domain decomposition, 81: 8 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 12 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.356 0.089 399.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 8.728 2.750 9.900 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (671 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.2%. 81: The balanceable part of the MD step is 46%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: 81: NOTE: 10 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.842 0.211 398.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 3.679 6.523 23.482 0.001 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (365 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 26.0%. 81: The balanceable part of the MD step is 38%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 9.9%. 81: 81: NOTE: 9.9 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 21 % of the run time was spent in domain decomposition, 81: 3 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.730 0.433 399.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 1.797 13.355 48.078 0.000 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (1068 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 21.8%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 11.0%. 81: 81: NOTE: 11.0 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 14 % of the run time was spent in domain decomposition, 81: 7 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 12 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.830 0.208 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 3.744 6.410 23.076 0.001 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (692 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: NVE simulation: will use the initial temperature of 246.451 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 8.0%. 81: The balanceable part of the MD step is 55%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 4.4%. 81: 81: 81: NOTE: 15 % of the run time was spent in domain decomposition, 81: 6 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 10 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.464 0.116 399.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 6.697 3.583 12.900 0.002 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (240 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 81: Parrinello-Rahman is not implemented in md-vv. 81: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 16 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 9 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.937 0.234 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 3.317 7.236 26.050 0.001 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (461 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.690 0.174 396.0 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.464 5.376 19.353 0.001 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (608 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vacuo.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 13 % of the run time was spent in domain decomposition, 81: 2 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.489 0.374 398.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 2.079 11.545 41.560 0.001 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (995 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 16 % of the run time was spent in domain decomposition, 81: 3 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 9 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.309 0.077 398.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 10.038 2.391 8.607 0.003 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (679 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 14 % of the run time was spent in domain decomposition, 81: 3 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 12 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.557 0.139 399.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 5.577 4.303 15.491 0.001 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (289 ms) 81: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 5 atoms that are fully frozen and part of COMM removal 81: group(s), removing these atoms from the COMM removal group(s) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: There are 3 atoms that are frozen along less then 3 dimensions and part 81: of COMM removal group(s), due to limitations in the code these still 81: contribute to the mass of the COM along frozen dimensions and therefore 81: the COMM correction will be too small. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 81: 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine-dipeptide' 81: 8 steps, 0.0 ps. 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 81: 81: turning H bonds into constraints... 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.722 0.194 371.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 4.002 5.997 21.590 0.001 81: 81: 81: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (359 ms) 81: [----------] 12 tests from FreezeWorks/FreezeGroupTest (6432 ms total) 81: 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -672408129 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 32.1%. 81: The balanceable part of the MD step is 31%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 9.8%. 81: 81: NOTE: 9.8 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 23 % of the run time was spent in domain decomposition, 81: 5 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.374 0.094 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 16.630 1.443 10.391 0.001 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (147 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -1012146849 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 16.9%. 81: The balanceable part of the MD step is 40%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 6.8%. 81: 81: NOTE: 6.8 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 24 % of the run time was spent in domain decomposition, 81: 5 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.389 0.097 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 15.974 1.502 10.818 0.001 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (144 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -63247365 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.2%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.6%. 81: 81: 81: NOTE: 28 % of the run time was spent in domain decomposition, 81: 9 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 9 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.800 0.216 370.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 7.201 3.333 23.997 0.000 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (344 ms) 81: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 81: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 81: on the accuracy of your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 81: < 0 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 81: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 81: Net Acceleration in X direction, will not be corrected 81: Net Acceleration in Y direction, will not be corrected 81: Net Acceleration in Z direction, will not be corrected 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 81: Can not increase nstlist because verlet-buffer-tolerance is not set or used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 3 non-bonded parameter combinations 81: 81: Generated 3 of the 3 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Setting gen_seed to -1158197377 81: 81: Velocities were taken from a Maxwell distribution at 0 K 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 9.1%. 81: The balanceable part of the MD step is 49%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 4.5%. 81: 81: 81: NOTE: 26 % of the run time was spent in domain decomposition, 81: 8 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.544 0.136 399.7 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 11.431 2.100 15.117 0.000 81: 81: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (219 ms) 81: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (855 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 31 tests from 9 test suites ran. (15650 ms total) 81: [ PASSED ] 30 tests. 81: [ SKIPPED ] 1 test, listed below: 81: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 81/104 Test #81: MdrunTestsTwoRanks ........................ Passed 15.68 sec test 82 Start 82: MdrunSingleRankAlgorithmsTests 82: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 82: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 600 82: [==========] Running 5 tests from 3 test suites. 82: [----------] Global test environment set-up. 82: [----------] 1 test from DispersionCorrectionTest 82: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 30.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: There are 9 non-linear virtual site constructions. Their contribution to 82: the energy error is approximated. In most cases this does not affect the 82: error significantly. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 82: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 82: 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Alanine dipeptide in vacuo' 82: 200 steps, 0.4 ps. 82: Setting the LD random seed to -9849410 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Converted 3 Bonds with virtual sites to connections, 7 left 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 12 Constraints with virtual sites to connections, 0 left 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.054 1.027 200.0 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 33.813 0.710 5.111 0.006 82: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (1078 ms) 82: [----------] 1 test from DispersionCorrectionTest (1078 ms total) 82: 82: [----------] 1 test from OriresTest 82: [ RUN ] OriresTest.OriresCanRun 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 518.00 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There was 1 NOTE 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2026.3-Debian_1 (double precision) 82: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 82: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 82: 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 82: 10 steps, 0.0 ps. 82: Setting the LD random seed to -92553863 82: 82: Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 82: 82: turning H bonds into constraints... 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: turning H bonds into constraints... 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/orires_1lvz.gro' 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.123 0.061 199.8 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 30.964 0.775 5.581 0.039 82: [ OK ] OriresTest.OriresCanRun (488 ms) 82: [----------] 1 test from OriresTest (488 ms total) 82: 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 82: Number of degrees of freedom in T-Coupling group rest is 10.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to -268763257 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: Searching the wall atom type(s) 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 17 % of the run time was spent in domain decomposition, 82: 3 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.135 0.068 199.8 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 67.200 0.357 3.214 0.001 82: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 82: 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (123 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 82: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 82: The supported numbers are > 1. 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 82: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 all molecules should be neutral. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: With epsilon_surface > 0 you can only use domain decomposition when there 82: are only small molecules with all bonds constrained (mdrun will check for 82: this). 82: 82: Number of degrees of freedom in T-Coupling group rest is 9.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: NVE simulation with an initial temperature of zero: will use a Verlet 82: buffer of 10%. Check your energy drift! 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Dipoles' 82: 20 steps, 0.1 ps. 82: Setting the LD random seed to -100735077 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Dipole' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 82: 82: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 10 % of the run time was spent in domain decomposition, 82: 14 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.125 0.063 198.3 82: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 82: Performance: 71.778 0.334 3.009 0.001 82: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 82: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (104 ms) 82: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (228 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 5 tests from 3 test suites ran. (1843 ms total) 82: [ PASSED ] 5 tests. 82/104 Test #82: MdrunSingleRankAlgorithmsTests ............ Passed 1.87 sec test 83 Start 83: Minimize1RankTests 83: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 2 test suites. 83: [----------] Global test environment set-up. 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -4.79910463671092e+01 83: Maximum force = 1.86297359432231e+02 on atom 13 83: Norm of force = 8.77219865482157e+01 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (632 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 3.02331e+02 on atom 3 83: F-Norm = 1.18024e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -5.58622538633302e+01 83: Maximum force = 4.27274822366368e+02 on atom 13 83: Norm of force = 1.84530029253754e+02 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (642 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.19376899751523e+02 83: Maximum force = 9.99884921009767e+03 on atom 9 83: Norm of force = 4.61669565054298e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (152 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: 83: NOTE 2 [file glycine_vacuo.top, line 12]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41575e+04 on atom 10 83: F-Norm = 1.18451e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.51743018140928e+02 83: Maximum force = 7.42089573409108e+03 on atom 9 83: Norm of force = 3.56929298615740e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (108 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.56984193848274e+02 83: Maximum force = 4.56923624626570e+02 on atom 17 83: Norm of force = 1.83258377168389e+02 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (86 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: 83: NOTE 3 [file unknown]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 1.06800e+03 on atom 28 83: F-Norm = 4.26922e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.69410778678181e+02 83: Maximum force = 2.18225948473987e+02 on atom 17 83: Norm of force = 7.92068036537548e+01 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (128 ms) 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1751 ms total) 83: 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents converged to Fmax < 10 in 1 steps 83: Potential Energy = -9.74257075835447e-01 83: Maximum force = 4.01322929015133e+00 on atom 1 83: Norm of force = 1.63839399694378e+00 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (15 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 83: Potential Energy = -9.90642313893957e-01 83: Maximum force = 2.57812909491104e+00 on atom 1 83: Norm of force = 1.05251679559258e+00 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (18 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 4.01323e+00 on atom 1 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 83: Potential Energy = -9.90642313893957e-01 83: Maximum force = 2.57812909491104e+00 on atom 1 83: Norm of force = 1.05251679559258e+00 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (18 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.19395484891520e+02 83: Maximum force = 9.97041707197911e+03 on atom 9 83: Norm of force = 4.62274878665467e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (116 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.56258793899480e+02 83: Maximum force = 7.50181017480397e+03 on atom 9 83: Norm of force = 3.61390332564874e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (108 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.3-Debian_1 (double precision) 83: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: 83: Low-Memory BFGS Minimizer: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: Using 10 BFGS correction steps. 83: 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization has stopped, but the forces have not converged to the 83: requested precision Fmax < 10 (which may not be possible for your system). It 83: stopped because the algorithm tried to make a new step whose size was too 83: small, or there was no change in the energy since last step. Either way, we 83: regard the minimization as converged to within the available machine 83: precision, given your starting configuration and EM parameters. 83: 83: writing lowest energy coordinates. 83: 83: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 83: but did not reach the requested Fmax < 10. 83: Potential Energy = 5.61116097794205e+02 83: Maximum force = 1.26854826291223e+04 on atom 10 83: Norm of force = 6.06436286976272e+03 83: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (183 ms) 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (463 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 2 test suites ran. (2239 ms total) 83: [ PASSED ] 12 tests. 83/104 Test #83: Minimize1RankTests ........................ Passed 2.28 sec test 84 Start 84: Minimize2RankTests 84: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 12 tests from 2 test suites. 84: [----------] Global test environment set-up. 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -4.79910463671093e+01 84: Maximum force = 1.86297359432232e+02 on atom 13 84: Norm of force = 8.77219865482159e+01 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (440 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 3.02331e+02 on atom 3 84: F-Norm = 1.18024e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -5.58622538633302e+01 84: Maximum force = 4.27274822366367e+02 on atom 13 84: Norm of force = 1.84530029253753e+02 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (638 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.19376899751523e+02 84: Maximum force = 9.99884921009767e+03 on atom 9 84: Norm of force = 4.61669565054298e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (223 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: 84: NOTE 2 [file glycine_vacuo.top, line 12]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 22.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41575e+04 on atom 10 84: F-Norm = 1.18451e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.51743018140927e+02 84: Maximum force = 7.42089573409111e+03 on atom 9 84: Norm of force = 3.56929298615739e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: turning H bonds into constraints... 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (279 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.56984193848274e+02 84: Maximum force = 4.56923624626570e+02 on atom 17 84: Norm of force = 1.83258377168389e+02 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (183 ms) 84: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: 84: NOTE 3 [file unknown]: 84: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 1.06800e+03 on atom 28 84: F-Norm = 4.26922e+02 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = -1.69410778678181e+02 84: Maximum force = 2.18225948473987e+02 on atom 17 84: Norm of force = 7.92068036537548e+01 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (296 ms) 84: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2062 ms total) 84: 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents converged to Fmax < 10 in 1 steps 84: Potential Energy = -9.74257075835447e-01 84: Maximum force = 4.01322929015133e+00 on atom 3 84: Norm of force = 1.63839399694378e+00 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (137 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 4.01323e+00 on atom 3 84: F-Norm = 1.63839e+00 84: 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 84: Potential Energy = -9.90642313893957e-01 84: Maximum force = 2.57812909491104e+00 on atom 3 84: Norm of force = 1.05251679559258e+00 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (49 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (3 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Steepest Descents: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Steepest Descents did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 3.19395484891520e+02 84: Maximum force = 9.97041707197911e+03 on atom 9 84: Norm of force = 4.62274878665467e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (213 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 84: Using 2 MPI threads 84: Using 2 OpenMP threads per tMPI thread 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Polak-Ribiere Conjugate Gradients: 84: Tolerance (Fmax) = 1.00000e+01 84: Number of steps = 4 84: F-max = 2.41672e+04 on atom 10 84: F-Norm = 1.19357e+04 84: 84: 84: Energy minimization reached the maximum number of steps before the forces 84: reached the requested precision Fmax < 10. 84: 84: writing lowest energy coordinates. 84: 84: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 84: Potential Energy = 1.56258793899480e+02 84: Maximum force = 7.50181017480397e+03 on atom 9 84: Norm of force = 3.61390332564874e+03 84: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (501 ms) 84: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 84: 84: Generating 1-4 interactions: fudge = 1 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Glycine' 84: 84: This run will generate roughly 0 Mb of data 84: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (64 ms) 84: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (972 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 12 tests from 2 test suites ran. (3060 ms total) 84: [ PASSED ] 12 tests. 84/104 Test #84: Minimize2RankTests ........................ Passed 3.09 sec test 85 Start 85: MdrunNonIntegratorTests 85: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 53 tests from 5 test suites. 85: [----------] Global test environment set-up. 85: [----------] 1 test from NonbondedBenchTest 85: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 85: SIMD width: 2 85: System size: 3000 atoms 85: Cut-off radius: 1 nm 85: Number of threads: 1 85: Number of iterations: 1 85: Compute energies: no 85: Ewald excl. corr.: analytical 85: 85: Coulomb LJ comb. SIMD intmod. Mcycles Mcycles/it. pairs/cycle 85: total useful 85: Ewald all geom. 4xM PotShift 0.441 0.4414 2.4008 1.4268 85: [ OK ] NonbondedBenchTest.BasicEndToEndTest (55 ms) 85: [----------] 1 test from NonbondedBenchTest (55 ms total) 85: 85: [----------] 5 tests from NormalModesWorks/NormalModesTest 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 15.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=6), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation '2 scaled waters' 85: 12 steps. 85: 85: Maximum force: 9.96989e-06 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.3-Debian_1 85: 85: Diagonalizing to find vectors 7 through 18... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--18 to eigenvec.trr 85: Generated 3 of the 3 non-bonded parameter combinations 85: 85: Generated 3 of the 3 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: This run will generate roughly 0 Mb of data 85: There are: 6 Atoms 85: Using begin = 7 and end = 18 85: Full matrix storage format, nrow=18, ncols=18 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (31 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 1 85: 85: NOTE 2 [file villin.top, line 2452]: 85: System has non-zero total charge: -2.000000 85: Total charge should normally be an integer. See 85: https://manual.gromacs.org/current/user-guide/floating-point.html 85: for discussion on how close it should be to an integer. 85: 85: 85: 85: Number of degrees of freedom in T-Coupling group System is 765.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=256), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 85: 512 steps. 85: 85: Maximum force: 6.97568e-04 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.3-Debian_1 85: 85: Diagonalizing to find vectors 7 through 50... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--50 to eigenvec.trr 85: Generated 20503 of the 20503 non-bonded parameter combinations 85: 85: Generated 17396 of the 20503 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 85: 85: This run will generate roughly 0 Mb of data 85: There are: 256 Atoms 85: Using begin = 7 and end = 50 85: Full matrix storage format, nrow=768, ncols=768 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (1853 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 15.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=6), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation 'flex spc dimer' 85: 12 steps. 85: 85: Maximum force: 3.36401e-04 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.3-Debian_1 85: 85: Diagonalizing to find vectors 7 through 18... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--18 to eigenvec.trr 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: This run will generate roughly 0 Mb of data 85: There are: 6 Atoms 85: Using begin = 7 and end = 18 85: Full matrix storage format, nrow=18, ncols=18 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (507 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 6.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 85: COM removal frequency is set to (4). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=3), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation '1 TIP5P' 85: 6 steps. 85: 85: Maximum force: 2.42882e-04 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.3-Debian_1 85: 85: Diagonalizing to find vectors 7 through 9... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--9 to eigenvec.trr 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: This run will generate roughly 0 Mb of data 85: There are: 3 Atoms 85: There are: 2 VSites 85: Using begin = 7 and end = 9 85: Full matrix storage format, nrow=9, ncols=9 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (802 ms) 85: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 85: Number of degrees of freedom in T-Coupling group System is 15.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There was 1 NOTE 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: 85: Small system size (N=6), using full Hessian format. 85: Allocating Hessian memory... 85: 85: starting normal mode calculation 'sw dimer' 85: 12 steps. 85: 85: Maximum force: 1.07599e-03 85: The force is probably not small enough to ensure that you are at a minimum. 85: Be aware that negative eigenvalues may occur 85: when the resulting matrix is diagonalized. 85: 85: 85: Writing Hessian... 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Reading double precision matrix generated by GROMACS 2026.3-Debian_1 85: 85: Diagonalizing to find vectors 7 through 18... 85: Writing eigenvalues... 85: 85: Writing average structure & eigenvectors 7--18 to eigenvec.trr 85: Generated 6 of the 10 non-bonded parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SW' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: This run will generate roughly 0 Mb of data 85: There are: 6 Atoms 85: There are: 2 Shells 85: There are: 2 VSites 85: 85: NOTE: in the current version shell prediction during the crun is disabled 85: 85: Using begin = 7 and end = 18 85: Full matrix storage format, nrow=18, ncols=18 85: Writing eigenfrequencies - negative eigenvalues will be set to zero. 85: Cannot compute entropy when -first = 7 85: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (144 ms) 85: [----------] 5 tests from NormalModesWorks/NormalModesTest (3342 ms total) 85: 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.114 0.057 199.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 25.650 0.936 3.368 0.004 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 85: 85: trr version: GMX_trn_file (double precision) 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 190.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4029.165 0.006 0.021 0.560 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (65 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.320 0.160 200.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 9.166 2.618 9.426 0.001 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 45 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.080 0.040 199.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 36.905 0.650 2.341 0.005 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (217 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.154 0.077 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 19.016 1.262 4.543 0.003 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 20 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 189.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3713.438 0.006 0.023 0.516 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (97 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There was 1 NOTE 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 161.606 0.149 0.535 0.022 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 189.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3886.810 0.006 0.022 0.540 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (30 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 181.611 0.132 0.476 0.032 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 188.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3375.668 0.007 0.026 0.586 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (755 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 85.702 0.280 1.008 0.015 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 22 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 189.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3779.505 0.006 0.023 0.656 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (459 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.139 0.069 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 21.161 1.134 4.083 0.004 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 25 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.000 190.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 3305.040 0.007 0.026 0.574 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (530 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.183 0.091 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 16.066 1.494 5.378 0.003 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 56 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 58.675 0.409 1.473 0.010 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (541 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.467 0.234 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 6.290 3.816 13.737 0.002 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 78 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.071 0.036 199.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 41.301 0.581 2.092 0.014 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (315 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 456.887 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 111.345 0.216 0.776 0.037 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 21 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 191.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 2185.383 0.011 0.040 0.734 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (37 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 137.781 0.174 0.627 0.046 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 44 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.089 0.045 199.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 32.945 0.728 2.623 0.011 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (189 ms) 85: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 2 [file unknown]: 85: You are using constraints on all bonds, whereas the forcefield has been 85: parametrized only with constraints involving hydrogen atoms. We suggest 85: using constraints = h-bonds instead, this will also improve performance. 85: 85: Number of degrees of freedom in T-Coupling group System is 23.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: There are 9 non-linear virtual site constructions. Their contribution to 85: the energy error is approximated. In most cases this does not affect the 85: error significantly. 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Alanine dipeptide in vacuo' 85: 16 steps, 0.0 ps. 85: Generated 2145 of the 2145 non-bonded parameter combinations 85: 85: Generated 2145 of the 2145 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 85: 85: turning all bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 85: 85: Cleaning up constraints and constant bonded interactions with virtual sites 85: 85: Removed 18 Angles with virtual sites, 21 left 85: 85: Removed 10 Proper Dih.s with virtual sites, 44 left 85: 85: Converted 15 Constraints with virtual sites to connections, 7 left 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.701 0.350 200.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 4.191 5.727 20.616 0.001 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 85: 85: Update groups can not be used for this system because an incompatible virtual site type is used 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 41 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.078 0.039 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 37.748 0.636 2.289 0.013 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (477 ms) 85: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (3720 ms total) 85: 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.216 0.108 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 13.623 1.762 6.342 0.006 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1644.579 0.015 0.053 0.685 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (135 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.042 0.021 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 69.481 0.345 1.244 0.029 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 54 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.074 0.037 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 39.769 0.603 2.173 0.017 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (108 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.200 0.100 199.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 14.640 1.639 5.901 0.006 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 53 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 198.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 47.528 0.505 1.818 0.020 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (164 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.070 0.035 199.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 41.639 0.576 2.075 0.017 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 54 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 47.935 0.501 1.802 0.020 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (105 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.217 0.109 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 13.527 1.774 6.387 0.006 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 55 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.060 0.030 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 48.843 0.491 1.769 0.020 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (169 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.332 0.166 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 8.843 2.714 9.770 0.004 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 60 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.070 0.035 199.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 41.880 0.573 2.063 0.017 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (235 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.194 0.097 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 15.139 1.585 5.707 0.006 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 81 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 197.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 208.990 0.115 0.413 0.087 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (132 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.219 0.110 199.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 13.375 1.794 6.460 0.006 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 52 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.112 0.056 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 26.190 0.916 3.299 0.011 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (199 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.197 0.098 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 14.924 1.608 5.789 0.006 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 174.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1690.613 0.014 0.051 0.704 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (139 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 11 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.287 0.144 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 10.220 2.348 8.454 0.004 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 180.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1420.801 0.017 0.061 0.592 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (189 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 198.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 111.793 0.215 0.773 0.047 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.012 0.006 195.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 242.257 0.099 0.357 0.101 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (53 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.301 0.150 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 9.760 2.459 8.853 0.004 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 176.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1535.925 0.016 0.056 0.640 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (193 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 44.928 0.534 1.923 0.019 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 175.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1679.093 0.014 0.051 0.700 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (71 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.027 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 53.918 0.445 1.602 0.022 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 78 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 197.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 151.728 0.158 0.569 0.063 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (74 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.015 199.5 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 94.973 0.253 0.910 0.040 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 175.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1689.686 0.014 0.051 0.704 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (47 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.159 0.079 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 18.500 1.297 4.670 0.008 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 173.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1607.671 0.015 0.054 0.670 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (122 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 123.555 0.194 0.699 0.051 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 175.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1314.961 0.018 0.066 0.548 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (51 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.400 0.200 200.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 7.334 3.272 11.781 0.003 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 54 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 199.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 47.755 0.503 1.809 0.020 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (269 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.264 0.132 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 11.111 2.160 7.776 0.005 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 53 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 199.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 49.351 0.486 1.751 0.021 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (189 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.311 0.156 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 9.442 2.542 9.150 0.004 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 65 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.131 0.066 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 22.335 1.075 3.868 0.009 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (257 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 70.656 0.340 1.223 0.029 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 60 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.101 0.050 199.4 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 29.100 0.825 2.969 0.012 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (123 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: NVE simulation: will use the initial temperature of 294.908 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.252 0.126 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 11.660 2.058 7.410 0.005 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 177.1 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1713.180 0.014 0.050 0.714 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (165 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.381 0.191 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 7.699 3.117 11.223 0.003 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 173.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1567.980 0.015 0.055 0.653 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (258 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.094 0.047 199.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 31.143 0.771 2.774 0.013 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.010 0.005 194.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 286.486 0.084 0.302 0.119 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (108 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 198.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 106.159 0.226 0.814 0.044 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.011 0.006 195.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 264.108 0.091 0.327 0.110 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (68 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 198.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 131.476 0.183 0.657 0.055 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 178.3 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1166.337 0.021 0.074 0.486 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (55 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.242 0.121 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 12.130 1.979 7.123 0.005 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 179.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1543.622 0.016 0.056 0.643 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (163 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 64.263 0.373 1.344 0.027 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 178.0 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1477.006 0.016 0.058 0.615 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (84 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.249 0.125 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 11.771 2.039 7.340 0.005 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 176.7 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 1595.182 0.015 0.054 0.665 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (191 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.364 0.182 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 8.070 2.974 10.707 0.003 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 55 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.072 0.036 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 40.624 0.591 2.127 0.017 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (280 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.267 0.133 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 11.012 2.179 7.846 0.005 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 51 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.032 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 46.001 0.522 1.878 0.019 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (204 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.243 0.122 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 12.065 1.989 7.161 0.005 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 58 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.112 0.056 199.6 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 26.260 0.914 3.290 0.011 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (226 ms) 85: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 79.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun '30 atom system in water' 85: 16 steps, 0.0 ps. 85: Generated 2485 of the 2485 non-bonded parameter combinations 85: 85: Generated 2485 of the 2485 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'nonanol' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.215 0.108 199.8 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 13.638 1.760 6.335 0.006 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 85: 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 85: 85: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 85: 85: NOTE: 48 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.067 0.034 199.2 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 43.499 0.552 1.986 0.018 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: 85: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (190 ms) 85: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (5032 ms total) 85: 85: [----------] 2 tests from Angles1/SimpleMdrunTest 85: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 85: 85: NOTE 1 [file angles1.top, line 72]: 85: In moleculetype 'butane' 4 atoms are not bound by a potential or 85: constraint to any other atom in the same moleculetype. Although 85: technically this might not cause issues in a simulation, this often means 85: that the user forgot to add a bond/potential/constraint or put multiple 85: molecules in the same moleculetype definition by mistake. Run with -v to 85: get information for each atom. 85: 85: Number of degrees of freedom in T-Coupling group System is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 238.919 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'This_incredible_box_of_butane' 85: 50 steps, 0.1 ps. 85: Generated 3 of the 3 non-bonded parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'butane' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/angles1.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.544 0.272 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 16.196 1.482 5.335 0.001 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 85: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (290 ms) 85: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 85: 85: NOTE 1 [file angles1.top, line 72]: 85: In moleculetype 'butane' 4 atoms are not bound by a potential or 85: constraint to any other atom in the same moleculetype. Although 85: technically this might not cause issues in a simulation, this often means 85: that the user forgot to add a bond/potential/constraint or put multiple 85: molecules in the same moleculetype definition by mistake. Run with -v to 85: get information for each atom. 85: 85: Number of degrees of freedom in T-Coupling group System is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 238.919 K for 85: determining the Verlet buffer size 85: 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'This_incredible_box_of_butane' 85: 50 steps, 0.1 ps. 85: Generated 3 of the 3 non-bonded parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'butane' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/angles1.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.286 0.143 199.9 85: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 85: Performance: 30.795 0.779 2.806 0.001 85: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 85: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (169 ms) 85: [----------] 2 tests from Angles1/SimpleMdrunTest (460 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 53 tests from 5 test suites ran. (12655 ms total) 85: [ PASSED ] 53 tests. 85/104 Test #85: MdrunNonIntegratorTests ................... Passed 12.69 sec test 86 Start 86: MdrunTpiTests 86: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 3 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 3 tests from Simple/TpiTest 86: [ RUN ] Simple/TpiTest.ReproducesOutput/0 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2026.3-Debian_1 (double precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/0 (430 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/1 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2026.3-Debian_1 (double precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/1 (359 ms) 86: [ RUN ] Simple/TpiTest.ReproducesOutput/2 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 1308.00 86: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2026.3-Debian_1 (double precision) 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Reading frames from gro file '216 water molecules', 648 atoms. 86: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 86: Last frame 0 time 0.000 86: Generated 331705 of the 331705 non-bonded parameter combinations 86: 86: Generated 331705 of the 331705 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Excluding 3 bonded neighbours molecule type 'methane' 86: Analysing residue names: 86: There are: 216 Water residues 86: There are: 1 Other residues 86: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] Simple/TpiTest.ReproducesOutput/2 (337 ms) 86: [----------] 3 tests from Simple/TpiTest (1133 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 3 tests from 1 test suite ran. (1141 ms total) 86: [ PASSED ] 3 tests. 86/104 Test #86: MdrunTpiTests ............................. Passed 1.17 sec test 87 Start 87: MdrunMpiTests 87: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 16 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from MimicTest 87: [ RUN ] MimicTest.OneQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 14 % of the run time was spent in domain decomposition, 87: 9 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 17 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 377.0 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 256.831 0.093 0.336 0.036 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -557029377 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.OneQuantumMol (354 ms) 87: [ RUN ] MimicTest.AllQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 40 % of the run time was spent in domain decomposition, 87: 13 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.070 0.017 398.8 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 4.953 4.845 17.443 0.001 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2113765367 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.AllQuantumMol (61 ms) 87: [ RUN ] MimicTest.TwoQuantumMol 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 21.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro' 87: 87: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 17 % of the run time was spent in domain decomposition, 87: 11 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.000 370.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 308.678 0.078 0.280 0.043 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -132385 87: 87: Generated 10 of the 10 non-bonded parameter combinations 87: 87: Generated 10 of the 10 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/4water.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.TwoQuantumMol (84 ms) 87: [ RUN ] MimicTest.BondCuts 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: For a correct single-point energy evaluation with nsteps = 0, use 87: continuation = yes to avoid constraining the input coordinates. 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 66.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: NVE simulation: will use the initial temperature of 300.368 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 87: 87: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 87: Reading frame 0 time 0.000 Last frame 0 time 0.000 87: 87: NOTE: 40 % of the run time was spent in domain decomposition, 87: 18 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.130 0.033 399.5 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 2.647 9.068 32.644 0.001 87: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -41992193 87: 87: Generated 2211 of the 2211 non-bonded parameter combinations 87: 87: Generated 2211 of the 2211 1-4 parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/ala.gro' 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] MimicTest.BondCuts (131 ms) 87: [----------] 4 tests from MimicTest (633 ms total) 87: 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: There was 1 NOTE 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There were 2 NOTEs 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 9.00 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 87: The optimal PME mesh load for parallel simulations is below 0.5 87: and for highly parallel simulations between 0.25 and 0.33, 87: for higher performance, increase the cut-off and the PME grid spacing. 87: 87: 87: 87: There was 1 NOTE 87: Setting the LD random seed to -486539846 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -1212164233 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to 2098457598 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: Setting the LD random seed to -828639237 87: 87: Generated 3 of the 3 non-bonded parameter combinations 87: 87: Generated 3 of the 3 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 87: 87: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 87: 87: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: Calculating fourier grid dimensions for X Y Z 87: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 87: 87: Estimate for the relative computational load of the PME mesh part: 1.00 87: 87: This run will generate roughly 0 Mb of data 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.7%. 87: The balanceable part of the MD step is 26%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 73 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.111 0.046 243.2 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 39.725 0.604 2.175 0.003 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (79 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.458 0.115 399.1 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 15.813 1.518 5.464 0.001 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (487 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot have separate PME ranks when PME is not used 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (3 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was turned on during the run due to measured imbalance. 87: Average load imbalance: 10.9%. 87: The balanceable part of the MD step is 22%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.4%. 87: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 4 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.487 0.372 399.8 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 4.880 4.918 17.706 0.000 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (480 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.524 0.381 399.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 4.762 5.040 18.144 0.000 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (786 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 13 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.950 0.738 399.9 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 2.459 9.758 35.129 0.000 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1407 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.3-Debian_1 (double precision) 87: Changing nstlist from 10 to 100, rlist from 1 to 1 87: 87: Using 2 MPI threads 87: Using 2 OpenMP threads per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.027 0.273 375.8 87: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 87: Performance: 6.638 3.616 13.017 0.000 87: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (346 ms) 87: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 87: Test configuration is invalid: 87: Cannot use two separate PME ranks when there are less than four ranks total 87: 87: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 87: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (3592 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 16 tests from 2 test suites ran. (4268 ms total) 87: [ PASSED ] 10 tests. 87: [ SKIPPED ] 6 tests, listed below: 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 87: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 87/104 Test #87: MdrunMpiTests ............................. Passed 4.29 sec test 88 Start 88: MdrunMultiSimTests 88: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 2 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from InNvt/MultiSimTerminationTest 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (1 ms) 88: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 88: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 88: [----------] 2 tests from InNvt/MultiSimTerminationTest (2 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 2 tests from 1 test suite ran. (12 ms total) 88: [ PASSED ] 2 tests. 88: 88: YOU HAVE 4 DISABLED TESTS 88: 88/104 Test #88: MdrunMultiSimTests ........................ Passed 0.04 sec test 89 Start 89: MdrunMultiSimReplexTests 89: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 1 test from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 89: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 89: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 89: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 1 test from 1 test suite ran. (15 ms total) 89: [ PASSED ] 1 test. 89: 89: YOU HAVE 4 DISABLED TESTS 89: 89/104 Test #89: MdrunMultiSimReplexTests .................. Passed 0.04 sec test 90 Start 90: MdrunMultiSimReplexEquivalenceTests 90: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 0 tests from 0 test suites. 90: [==========] 0 tests from 0 test suites ran. (2 ms total) 90: [ PASSED ] 0 tests. 90: 90: YOU HAVE 10 DISABLED TESTS 90: 90/104 Test #90: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.03 sec test 91 Start 91: MdrunMpi1RankPmeTests 91: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 91: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 19 tests from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 19 tests from ReproducesEnergies/PmeTest 91: Number of degrees of freedom in T-Coupling group rest is 12.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 1046.791 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 2 NOTEs 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: For a correct single-point energy evaluation with nsteps = 0, use 91: continuation = yes to avoid constraining the input coordinates. 91: 91: Number of degrees of freedom in T-Coupling group rest is 13.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 966.268 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 3 NOTEs 91: Setting the LD random seed to -1518612516 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: Setting the LD random seed to -62919939 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: Searching the wall atom type(s) 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.560 0.280 199.9 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 6.480 3.704 13.334 0.000 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (323 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.526 0.263 199.9 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 6.898 3.479 12.526 0.000 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (293 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: NOTE: 28 % of the run time was spent in domain decomposition, 91: 9 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.045 0.022 199.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 3.850 6.234 22.443 0.000 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (51 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets using PME rank(s) but the simulation is using only one rank 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.498 0.249 200.0 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 7.283 3.295 11.863 0.001 91: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (270 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [----------] 19 tests from ReproducesEnergies/PmeTest (946 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 19 tests from 1 test suite ran. (973 ms total) 91: [ PASSED ] 4 tests. 91: [ SKIPPED ] 15 tests, listed below: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91/104 Test #91: MdrunMpi1RankPmeTests ..................... Passed 1.01 sec test 92 Start 92: MdrunMpi2RankPmeTests 92: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 19 tests from 1 test suite. 92: [----------] Global test environment set-up. 92: [----------] 19 tests from ReproducesEnergies/PmeTest 92: Number of degrees of freedom in T-Coupling group rest is 12.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 1046.791 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 2 NOTEs 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: For a correct single-point energy evaluation with nsteps = 0, use 92: continuation = yes to avoid constraining the input coordinates. 92: 92: Number of degrees of freedom in T-Coupling group rest is 13.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 966.268 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 3 NOTEs 92: Setting the LD random seed to -18350083 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: Setting the LD random seed to -11897089 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: Searching the wall atom type(s) 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.8%. 92: The balanceable part of the MD step is 20%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.8%. 92: 92: 92: NOTE: 9 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 2.038 0.510 399.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 3.560 6.741 24.268 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (585 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 12.5%. 92: The balanceable part of the MD step is 26%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.3%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: 92: 92: NOTE: 24 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.931 0.483 399.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 3.757 6.388 22.997 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (1024 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (1 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 28 % of the run time was spent in domain decomposition, 92: 8 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.090 0.023 391.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 3.746 6.407 23.065 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (436 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.572 0.410 383.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 4.427 5.422 19.517 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (514 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.161 0.290 399.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 6.251 3.839 13.822 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (608 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (2 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 20 % of the run time was spent in domain decomposition, 92: 14 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.064 0.016 395.6 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 5.307 4.522 16.279 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (238 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 2 MPI threads 92: Using 2 OpenMP threads per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 9.4%. 92: The balanceable part of the MD step is 32%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.0%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: 92: 92: NOTE: 24 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.966 0.492 400.0 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 3.691 6.503 23.411 0.000 92: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (731 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [----------] 19 tests from ReproducesEnergies/PmeTest (4153 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 19 tests from 1 test suite ran. (4177 ms total) 92: [ PASSED ] 7 tests. 92: [ SKIPPED ] 12 tests, listed below: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92/104 Test #92: MdrunMpi2RankPmeTests ..................... Passed 4.21 sec test 93 Start 93: MdrunMpi4RankPmeTests 93: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "1" "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunMpi4RankPmeTests.xml" 93: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 93: Test timeout computed to be: 600 93: [==========] Running 19 tests from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 19 tests from ReproducesEnergies/PmeTest 93: Number of degrees of freedom in T-Coupling group rest is 12.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 1046.791 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 2 NOTEs 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: For a correct single-point energy evaluation with nsteps = 0, use 93: continuation = yes to avoid constraining the input coordinates. 93: 93: Number of degrees of freedom in T-Coupling group rest is 13.00 93: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: NVE simulation: will use the initial temperature of 966.268 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 93: The optimal PME mesh load for parallel simulations is below 0.5 93: and for highly parallel simulations between 0.25 and 0.33, 93: for higher performance, increase the cut-off and the PME grid spacing. 93: 93: 93: 93: There were 3 NOTEs 93: Setting the LD random seed to -16795665 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: Setting the LD random seed to -67371139 93: 93: Generated 8 of the 10 non-bonded parameter combinations 93: 93: Excluding 2 bonded neighbours molecule type 'Methanol' 93: 93: Excluding 2 bonded neighbours molecule type 'SOL' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc-and-methanol.gro' 93: 93: Searching the wall atom type(s) 93: 93: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 93: 93: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 93: 93: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: Calculating fourier grid dimensions for X Y Z 93: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 93: 93: Estimate for the relative computational load of the PME mesh part: 1.00 93: 93: This run will generate roughly 0 Mb of data 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was turned on during the run due to measured imbalance. 93: Average load imbalance: 23.2%. 93: The balanceable part of the MD step is 20%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 4.7%. 93: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 93: 93: 93: NOTE: 20 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 2.757 0.689 400.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 2.632 9.117 32.821 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (1447 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was turned on during the run due to measured imbalance. 93: Average load imbalance: 29.8%. 93: The balanceable part of the MD step is 20%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 6.0%. 93: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 93: 93: NOTE: 6.0 % of the available CPU time was lost due to load imbalance 93: in the domain decomposition. 93: You can consider manually changing the decomposition (option -dd); 93: e.g. by using fewer domains along the box dimension in which there is 93: considerable inhomogeneity in the simulated system. 93: 93: NOTE: 26 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 3.975 0.994 400.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 1.825 13.147 47.330 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (1575 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: NOTE: 25 % of the run time was spent in domain decomposition, 93: 0 % of the run time was spent in pair search, 93: you might want to increase nstlist (this has no effect on accuracy) 93: 93: NOTE: 18 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.415 0.120 346.7 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 0.721 33.277 119.798 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (838 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was off during the run due to low measured imbalance. 93: Average load imbalance: 3.8%. 93: The balanceable part of the MD step is 11%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 0.4%. 93: Average PME mesh/force load: 138.162 93: Part of the total run time spent waiting due to PP/PME imbalance: 52.3 % 93: 93: NOTE: 52.3 % performance was lost because the PME ranks 93: had more work to do than the PP ranks. 93: You might want to increase the number of PME ranks 93: or increase the cut-off and the grid spacing. 93: 93: 93: NOTE: 38 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.462 0.134 343.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 13.513 1.776 6.394 0.001 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (247 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was turned on during the run due to measured imbalance. 93: Average load imbalance: 4.1%. 93: The balanceable part of the MD step is 66%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 2.7%. 93: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 93: Average PME mesh/force load: 0.386 93: Part of the total run time spent waiting due to PP/PME imbalance: 1.2 % 93: 93: 93: NOTE: 11 % of the run time was spent in domain decomposition, 93: 0 % of the run time was spent in pair search, 93: you might want to increase nstlist (this has no effect on accuracy) 93: 93: NOTE: 38 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 2.267 0.567 400.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 3.201 7.498 26.993 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (1198 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.3-Debian_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 0 steps, 0.0 ps. 93: 93: NOTE: 53 % of the run time was spent in domain decomposition, 93: 0 % of the run time was spent in pair search, 93: you might want to increase nstlist (this has no effect on accuracy) 93: 93: NOTE: 13 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.296 0.090 329.3 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 0.960 24.993 89.974 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (977 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 93: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.3-Debian_1 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 4 MPI threads 93: Using 1 OpenMP thread per tMPI thread 93: 93: 93: NOTE: The number of threads is not equal to the number of (logical) cpus 93: and the -pin option is set to auto: will not pin threads to cpus. 93: This can lead to significant performance degradation. 93: Consider using -pin on (and -pinoffset in case you run multiple jobs). 93: starting mdrun 'spc-and-methanol' 93: 20 steps, 0.0 ps. 93: 93: Writing final coordinates. 93: 93: 93: Dynamic load balancing report: 93: DLB was turned on during the run due to measured imbalance. 93: Average load imbalance: 16.2%. 93: The balanceable part of the MD step is 19%, load imbalance is computed from this. 93: Part of the total run time spent waiting due to load imbalance: 3.0%. 93: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 93: 93: 93: NOTE: 21 % of the run time was spent communicating energies, 93: you might want to increase some nst* mdp options 93: 93: Core t (s) Wall t (s) (%) 93: Time: 5.276 1.325 398.2 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 1.369 17.527 63.098 0.000 93: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (2454 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 93: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 93: Test is being skipped because: 93: it targets GPU execution, but no compatible devices were detected 93: it targets PME decomposition, but that is not supported 93: it targets GPU execution of FFT work, which is not supported in the current build 93: PME GPU does not support: 93: Double-precision build of GROMACS. 93: Non-GPU build of GROMACS. 93: Current GPU backend. 93: 93: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 93: [----------] 19 tests from ReproducesEnergies/PmeTest (8743 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 19 tests from 1 test suite ran. (9070 ms total) 93: [ PASSED ] 7 tests. 93: [ SKIPPED ] 12 tests, listed below: 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 93: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 93/104 Test #93: MdrunMpi4RankPmeTests ..................... Passed 9.10 sec test 94 Start 94: MdrunCoordinationBasicTests1Rank 94: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 94: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 94: Test timeout computed to be: 1920 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest 94: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.011 0.011 99.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 131.356 0.183 0.658 0.018 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.010 0.010 99.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 144.574 0.166 0.598 0.020 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 4. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 4. 94: 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.004 0.004 98.8 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 411.310 0.058 0.210 0.057 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.007 0.007 99.4 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 203.025 0.118 0.426 0.028 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.010 0.010 99.5 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 151.091 0.159 0.572 0.021 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 1 MPI thread 94: Using 1 OpenMP thread 94: 94: 94: NOTE: Thread affinity was not set. 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.005 0.005 99.1 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 302.940 0.079 0.285 0.042 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (109 ms) 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest (111 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (132 ms total) 94: [ PASSED ] 1 test. 94/104 Test #94: MdrunCoordinationBasicTests1Rank .......... Passed 0.16 sec test 95 Start 95: MdrunCoordinationBasicTests2Ranks 95: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 95: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 95: Test timeout computed to be: 1920 95: [==========] Running 1 test from 1 test suite. 95: [----------] Global test environment set-up. 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest 95: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was turned on during the run due to measured imbalance. 95: Average load imbalance: 17.5%. 95: The balanceable part of the MD step is 50%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 8.7%. 95: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 95: 95: NOTE: 8.7 % of the available CPU time was lost due to load imbalance 95: in the domain decomposition. 95: You can consider manually changing the decomposition (option -dd); 95: e.g. by using fewer domains along the box dimension in which there is 95: considerable inhomogeneity in the simulated system. 95: 95: NOTE: 11 % of the run time was spent in domain decomposition, 95: 0 % of the run time was spent in pair search, 95: you might want to increase nstlist (this has no effect on accuracy) 95: 95: NOTE: 32 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.520 0.261 199.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 5.630 4.263 15.345 0.001 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 2.2%. 95: The balanceable part of the MD step is 47%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 1.1%. 95: 95: 95: NOTE: 48 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.025 0.012 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 119.142 0.201 0.725 0.017 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 3.1%. 95: The balanceable part of the MD step is 42%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 1.3%. 95: 95: 95: NOTE: 50 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.024 0.012 199.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 122.341 0.196 0.706 0.017 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 2.4%. 95: The balanceable part of the MD step is 41%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 1.0%. 95: 95: 95: NOTE: 49 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.023 0.011 198.9 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 129.278 0.186 0.668 0.018 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 2.6%. 95: The balanceable part of the MD step is 37%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 1.0%. 95: 95: 95: NOTE: 49 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.035 0.017 199.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 84.428 0.284 1.023 0.012 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (1). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 2 MPI threads 95: Using 1 OpenMP thread per tMPI thread 95: 95: 95: NOTE: The number of threads is not equal to the number of (logical) cpus 95: and the -pin option is set to auto: will not pin threads to cpus. 95: This can lead to significant performance degradation. 95: Consider using -pin on (and -pinoffset in case you run multiple jobs). 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: 95: Dynamic load balancing report: 95: DLB was off during the run due to low measured imbalance. 95: Average load imbalance: 1.8%. 95: The balanceable part of the MD step is 32%, load imbalance is computed from this. 95: Part of the total run time spent waiting due to load imbalance: 0.6%. 95: 95: 95: NOTE: 48 % of the run time was spent communicating energies, 95: you might want to increase some nst* mdp options 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.033 0.017 199.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 87.636 0.274 0.986 0.012 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1604 ms) 95: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1604 ms total) 95: 95: [----------] Global test environment tear-down 95: [==========] 1 test from 1 test suite ran. (1625 ms total) 95: [ PASSED ] 1 test. 95/104 Test #95: MdrunCoordinationBasicTests2Ranks ......... Passed 1.66 sec test 96 Start 96: MdrunCoordinationCouplingTests1Rank 96: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 96: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 96: Test timeout computed to be: 1920 96: [==========] Running 25 tests from 1 test suite. 96: [----------] Global test environment set-up. 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.023 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 64.351 0.373 1.343 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 241.924 0.099 0.357 0.034 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.425 0.129 0.463 0.026 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 118.818 0.202 0.727 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.013 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 117.340 0.205 0.736 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 291.502 0.082 0.296 0.040 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (141 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 139.982 0.171 0.617 0.019 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.133 0.126 0.452 0.027 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 98.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 389.123 0.062 0.222 0.054 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.057 0.057 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 25.753 0.932 3.355 0.004 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 293.431 0.082 0.294 0.041 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.168 0.126 0.452 0.027 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (175 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 115.298 0.208 0.749 0.016 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 131.244 0.183 0.658 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 131.789 0.182 0.656 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 122.343 0.196 0.706 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 165.969 0.145 0.521 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 145.126 0.165 0.595 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (132 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 180.954 0.133 0.477 0.025 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 331.625 0.072 0.261 0.046 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.025 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 58.474 0.410 1.478 0.008 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.119 0.119 100.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 12.325 1.947 7.010 0.002 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.056 0.056 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 26.013 0.923 3.321 0.004 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 174.729 0.137 0.494 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (339 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 163.959 0.146 0.527 0.023 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 319.865 0.075 0.270 0.044 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 157.379 0.152 0.549 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 230.630 0.104 0.375 0.032 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 121.131 0.198 0.713 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.295 0.123 0.442 0.027 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (132 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 116.306 0.206 0.743 0.016 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 238.367 0.101 0.362 0.033 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 339.651 0.071 0.254 0.047 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.008 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 195.761 0.123 0.441 0.027 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 121.773 0.197 0.710 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 203.179 0.118 0.425 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (128 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.006 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 266.877 0.090 0.324 0.037 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 159.300 0.151 0.542 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 98.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 391.000 0.061 0.221 0.054 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 136.650 0.176 0.632 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 201.709 0.119 0.428 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 167.040 0.144 0.517 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (111 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 122.748 0.196 0.704 0.017 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 99.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 341.913 0.070 0.253 0.047 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 138.406 0.173 0.624 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 158.333 0.152 0.546 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 122.477 0.196 0.705 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 235.884 0.102 0.366 0.033 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (107 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.059 0.059 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 24.865 0.965 3.475 0.003 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.025 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 57.851 0.415 1.493 0.008 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 313.325 0.077 0.276 0.044 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 183.362 0.131 0.471 0.025 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.015 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 97.493 0.246 0.886 0.014 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 186.199 0.129 0.464 0.026 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (197 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 157.859 0.152 0.547 0.022 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 98.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 339.109 0.071 0.255 0.047 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 234.520 0.102 0.368 0.033 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 151.492 0.158 0.570 0.021 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.116 0.116 100.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 12.708 1.889 6.799 0.002 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 201.327 0.119 0.429 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (214 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 311.110 0.077 0.278 0.043 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 153.302 0.157 0.564 0.021 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 161.555 0.149 0.535 0.022 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 275.014 0.087 0.314 0.038 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 99.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 334.869 0.072 0.258 0.047 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.528 0.117 0.422 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (106 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.016 0.016 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.198 0.266 0.958 0.013 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 306.116 0.078 0.282 0.043 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 270.237 0.089 0.320 0.038 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 98.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 329.496 0.073 0.262 0.046 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.646 0.134 0.481 0.025 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 153.176 0.157 0.564 0.021 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (104 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 113.723 0.211 0.760 0.016 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 99.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 391.397 0.061 0.221 0.054 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.123 0.123 100.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 11.932 2.011 7.241 0.002 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 294.596 0.081 0.293 0.041 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.004 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 333.763 0.072 0.259 0.046 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 242.906 0.099 0.356 0.034 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (220 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 220.976 0.109 0.391 0.031 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 256.948 0.093 0.336 0.036 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 135.071 0.178 0.640 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 111.633 0.215 0.774 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 170.300 0.141 0.507 0.024 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 179.478 0.134 0.481 0.025 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (118 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 152.121 0.158 0.568 0.021 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.004 0.005 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 325.355 0.074 0.266 0.045 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.014 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 108.457 0.221 0.797 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 111.116 0.216 0.778 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.067 0.067 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 21.928 1.095 3.940 0.003 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.049 0.049 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 30.185 0.795 2.862 0.004 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (207 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 101.870 0.236 0.848 0.014 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 272.243 0.088 0.317 0.038 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.030 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 49.511 0.485 1.745 0.007 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 134.253 0.179 0.644 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 111.048 0.216 0.778 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.026 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 56.516 0.425 1.529 0.008 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (140 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.027 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 53.775 0.446 1.607 0.007 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.017 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 85.340 0.281 1.012 0.012 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.018 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 83.531 0.287 1.034 0.012 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 120.120 0.200 0.719 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 127.927 0.188 0.675 0.018 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 135.843 0.177 0.636 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (146 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.017 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 85.025 0.282 1.016 0.012 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.019 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 79.195 0.303 1.091 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 146.691 0.164 0.589 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.016 0.017 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.998 0.270 0.971 0.012 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.027 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 53.958 0.445 1.601 0.007 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.052 0.052 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 28.297 0.848 3.053 0.004 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (208 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.044 0.044 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 33.228 0.722 2.600 0.005 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.025 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 59.869 0.401 1.443 0.008 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.035 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 42.413 0.566 2.037 0.006 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 253.293 0.095 0.341 0.035 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.067 0.067 100.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 22.036 1.089 3.921 0.003 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 106.977 0.224 0.808 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (266 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 188.340 0.127 0.459 0.026 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 238.127 0.101 0.363 0.033 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.016 0.017 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.951 0.270 0.971 0.012 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 163.867 0.146 0.527 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.009 0.009 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 162.875 0.147 0.530 0.023 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 134.540 0.178 0.642 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (114 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 128.718 0.186 0.671 0.018 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.008 0.008 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 181.836 0.132 0.475 0.025 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 97.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 299.174 0.080 0.289 0.042 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 148.681 0.161 0.581 0.021 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 110.361 0.217 0.783 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 133.958 0.179 0.645 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (109 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.017 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 85.586 0.280 1.010 0.012 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.022 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 66.179 0.363 1.306 0.009 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.027 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 54.181 0.443 1.595 0.008 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 140.243 0.171 0.616 0.019 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 140.826 0.170 0.614 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.006 0.006 99.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 238.210 0.101 0.363 0.033 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (165 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.011 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 128.880 0.186 0.670 0.018 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.007 0.007 99.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 204.650 0.117 0.422 0.028 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.013 99.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 113.723 0.211 0.760 0.016 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.019 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 75.749 0.317 1.141 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.029 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 50.057 0.479 1.726 0.007 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 106.281 0.226 0.813 0.015 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (154 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 29 % of the run time was spent in pair search, 96: you might want to increase nstlist (this has no effect on accuracy) 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.014 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 106.206 0.226 0.814 0.015 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.005 0.005 98.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 300.502 0.080 0.288 0.042 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.020 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.167 0.333 1.197 0.010 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 122.256 0.196 0.707 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.023 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 63.982 0.375 1.350 0.009 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.033 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 43.878 0.547 1.969 0.006 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (168 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.041 0.042 98.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 34.950 0.687 2.472 0.005 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.021 99.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 68.744 0.349 1.257 0.010 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.012 0.012 99.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 119.549 0.201 0.723 0.017 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.033 99.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 43.863 0.547 1.970 0.006 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.010 0.010 99.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 141.943 0.169 0.609 0.020 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 96: 96: Using 1 MPI thread 96: Using 1 OpenMP thread 96: 96: 96: NOTE: Thread affinity was not set. 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.019 99.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 76.930 0.312 1.123 0.011 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (214 ms) 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (4126 ms total) 96: 96: [----------] Global test environment tear-down 96: [==========] 25 tests from 1 test suite ran. (4147 ms total) 96: [ PASSED ] 25 tests. 96/104 Test #96: MdrunCoordinationCouplingTests1Rank ....... Passed 4.18 sec test 97 Start 97: MdrunCoordinationCouplingTests2Ranks 97: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 97: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 97: Test timeout computed to be: 1920 97: [==========] Running 25 tests from 1 test suite. 97: [----------] Global test environment set-up. 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.048 0.024 199.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 61.556 0.390 1.404 0.009 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 20.7%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 10.6%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 10.6 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 13 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 53 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.837 0.418 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.510 6.837 24.613 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.1%. 97: The balanceable part of the MD step is 37%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 244.361 0.098 0.354 0.034 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 33.3%. 97: The balanceable part of the MD step is 10%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 3.2%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.221 0.111 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 13.273 1.808 6.509 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.4%. 97: The balanceable part of the MD step is 34%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 181.335 0.132 0.476 0.025 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 3.4%. 97: The balanceable part of the MD step is 34%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.046 0.023 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 63.586 0.377 1.359 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1628 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 13.6%. 97: The balanceable part of the MD step is 53%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 7.3%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 7.3 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 10 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 38 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.787 0.893 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.644 14.597 52.551 0.000 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.7%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.3%. 97: 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.128 0.064 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 23.006 1.043 3.756 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 3.1%. 97: The balanceable part of the MD step is 31%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.290 0.145 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 10.121 2.371 8.537 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.4%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 57 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.150 0.075 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 19.615 1.224 4.405 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.3%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 75 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.039 0.035 109.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 41.650 0.576 2.074 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.9%. 97: The balanceable part of the MD step is 35%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.0%. 97: 97: 97: NOTE: 60 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.012 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 127.603 0.188 0.677 0.018 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2768 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 50%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 55 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 194.989 0.123 0.443 0.027 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 32.2%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 14.8%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 14.8 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 36 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.074 0.037 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 39.384 0.609 2.194 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.7%. 97: The balanceable part of the MD step is 40%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 161.420 0.149 0.535 0.022 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.2%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 211.843 0.113 0.408 0.029 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.2%. 97: The balanceable part of the MD step is 40%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 97.950 0.245 0.882 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.8%. 97: The balanceable part of the MD step is 39%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 143.922 0.167 0.600 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (343 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.4%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 195.705 0.123 0.441 0.027 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 41%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.024 0.012 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 124.115 0.193 0.696 0.017 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.1%. 97: The balanceable part of the MD step is 37%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.028 0.014 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 106.153 0.226 0.814 0.015 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.0%. 97: The balanceable part of the MD step is 31%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.089 0.044 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.055 0.726 2.614 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 38%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.011 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 128.370 0.187 0.673 0.018 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.7%. 97: The balanceable part of the MD step is 37%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.011 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 139.702 0.172 0.618 0.019 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (976 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 51 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 198.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 217.159 0.111 0.398 0.030 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 215.304 0.111 0.401 0.030 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 76 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.037 0.034 106.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 42.844 0.560 2.017 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 44 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.678 0.339 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 4.331 5.542 19.951 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.078 0.039 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 37.429 0.641 2.308 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.046 0.023 199.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 63.851 0.376 1.353 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1342 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.009 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 155.357 0.154 0.556 0.022 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.005 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 271.022 0.089 0.319 0.038 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 46 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 26 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.030 146.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 48.945 0.490 1.765 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 77 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.046 0.023 197.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 63.229 0.380 1.366 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.039 0.020 199.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 74.578 0.322 1.159 0.010 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 72 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 143.213 0.168 0.603 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (983 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.047 0.023 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 62.929 0.381 1.373 0.009 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 57 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.031 0.015 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 95.016 0.253 0.909 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.120 0.060 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 24.479 0.980 3.529 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.112 0.056 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 26.128 0.919 3.307 0.004 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.023 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 64.814 0.370 1.333 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 55 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.013 0.007 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 216.712 0.111 0.399 0.030 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (961 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 27 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 129.716 0.185 0.666 0.018 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 45 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 246.685 0.097 0.350 0.034 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 56 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.919 0.460 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.194 7.513 27.047 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.008 0.520 194.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.827 8.490 30.566 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 72 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.035 121.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 41.507 0.578 2.082 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.024 0.012 191.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 119.332 0.201 0.724 0.017 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2391 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.025 0.013 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 115.400 0.208 0.749 0.016 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 75 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 100.492 0.239 0.860 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.026 0.013 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 112.659 0.213 0.767 0.016 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.010 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 140.797 0.170 0.614 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 68 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.008 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 188.213 0.128 0.459 0.026 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 234.395 0.102 0.369 0.033 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (975 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 52 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.024 0.012 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 122.881 0.195 0.703 0.017 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 98.693 0.243 0.875 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 61 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.006 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 233.683 0.103 0.370 0.032 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 143.602 0.167 0.602 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.015 0.007 196.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 195.857 0.123 0.441 0.027 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 74 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.039 0.027 142.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 54.004 0.444 1.600 0.008 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (793 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 67 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.069 0.050 136.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 29.187 0.822 2.960 0.004 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.033 0.017 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 87.388 0.275 0.989 0.012 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 31 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 43 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.181 0.090 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 16.263 1.476 5.313 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 66 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 97.123 0.247 0.890 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 52 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 100.743 0.238 0.858 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.032 0.016 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 91.393 0.263 0.945 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1375 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 135.478 0.177 0.638 0.019 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 59 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.960 0.490 196.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.999 8.003 28.812 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 59 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.936 0.484 193.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 3.035 7.907 28.467 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.025 0.013 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 116.720 0.206 0.740 0.016 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 67 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.097 0.064 150.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 22.794 1.053 3.790 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 97: 1 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 59 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.026 0.013 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 110.568 0.217 0.781 0.015 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2091 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 129.947 0.185 0.665 0.018 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 76 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.067 0.053 125.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 27.575 0.870 3.133 0.004 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.110 0.055 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 26.624 0.901 3.245 0.004 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 24 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.626 0.313 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 4.689 5.119 18.427 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.035 0.017 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 84.478 0.284 1.023 0.012 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 133.756 0.179 0.646 0.019 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1687 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 50 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.175 0.088 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 16.736 1.434 5.163 0.002 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 81 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.027 0.029 91.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 50.113 0.479 1.724 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.017 0.008 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 173.952 0.138 0.497 0.024 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 28 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 47 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 132.284 0.181 0.653 0.018 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 61 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.031 0.015 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 94.861 0.253 0.911 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 163.166 0.147 0.530 0.023 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (643 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 80 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.045 94.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.408 0.741 2.666 0.005 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 53 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 134.683 0.178 0.642 0.019 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 63 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.031 0.016 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 93.532 0.257 0.924 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.029 0.514 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.855 8.406 30.262 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 63 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 97.765 0.245 0.884 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.011 194.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 137.186 0.175 0.630 0.019 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1481 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.032 0.016 199.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 92.359 0.260 0.935 0.013 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 79 % of the run time was spent in domain decomposition, 97: 0 % of the run time was spent in pair search, 97: you might want to increase nstlist (this has no effect on accuracy) 97: 97: NOTE: 7 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.070 0.035 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 41.709 0.575 2.072 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 198.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 182.558 0.131 0.473 0.025 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 52 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 199.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 99.186 0.242 0.871 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 49 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.012 199.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 125.684 0.191 0.687 0.017 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 56 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.011 0.006 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 259.328 0.093 0.333 0.036 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1352 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.0%. 97: The balanceable part of the MD step is 56%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: NOTE: 36 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.185 0.108 170.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 13.588 1.766 6.359 0.002 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 53%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.016 0.008 197.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 184.294 0.130 0.469 0.026 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.7%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.025 0.013 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 114.219 0.210 0.756 0.016 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.6%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.2%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.021 0.020 101.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 72.016 0.333 1.200 0.010 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.8%. 97: The balanceable part of the MD step is 42%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.015 145.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 96.051 0.250 0.900 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.6%. 97: The balanceable part of the MD step is 42%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.7%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.038 0.029 130.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 50.652 0.474 1.706 0.007 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (757 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 9.5%. 97: The balanceable part of the MD step is 65%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 6.1%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 6.1 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 46 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 2.764 1.382 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.063 22.585 81.305 0.000 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.7%. 97: The balanceable part of the MD step is 53%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: NOTE: 7 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.581 0.318 182.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 4.618 5.197 18.711 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.9%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.189 0.095 199.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 15.498 1.549 5.575 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.0%. 97: The balanceable part of the MD step is 46%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.5%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.064 0.032 195.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 45.201 0.531 1.911 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.1%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.5%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.156 0.079 197.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 18.512 1.296 4.667 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.3%. 97: The balanceable part of the MD step is 48%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.6%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.052 0.038 138.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 39.164 0.613 2.206 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (3884 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 0.7%. 97: The balanceable part of the MD step is 38%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.2%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.155 0.078 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 18.901 1.270 4.571 0.003 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 11.9%. 97: The balanceable part of the MD step is 68%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 8.1%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 8.1 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 39 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.064 0.544 195.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 2.701 8.887 31.994 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.1%. 97: The balanceable part of the MD step is 51%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 1.1%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 197.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 148.801 0.161 0.581 0.021 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 2.1%. 97: The balanceable part of the MD step is 44%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.9%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.037 0.019 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 79.002 0.304 1.094 0.011 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was turned on during the run due to measured imbalance. 97: Average load imbalance: 10.9%. 97: The balanceable part of the MD step is 65%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 7.1%. 97: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 97: 97: NOTE: 7.1 % of the available CPU time was lost due to load imbalance 97: in the domain decomposition. 97: You can consider manually changing the decomposition (option -dd); 97: e.g. by using fewer domains along the box dimension in which there is 97: considerable inhomogeneity in the simulated system. 97: 97: NOTE: 48 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 2.337 1.173 199.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.252 19.170 69.010 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 97: NVE simulation: will use the initial temperature of 68.810 K for 97: determining the Verlet buffer size 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: 97: Dynamic load balancing report: 97: DLB was off during the run due to low measured imbalance. 97: Average load imbalance: 1.8%. 97: The balanceable part of the MD step is 45%, load imbalance is computed from this. 97: Part of the total run time spent waiting due to load imbalance: 0.8%. 97: 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.021 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 69.783 0.344 1.238 0.010 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (2799 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.026 0.016 161.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 92.791 0.259 0.931 0.013 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.014 0.007 192.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 202.678 0.118 0.426 0.028 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.026 0.013 198.1 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 110.273 0.218 0.784 0.015 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 42 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.518 0.759 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.934 12.408 44.668 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 35 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.272 0.158 172.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 9.306 2.579 9.284 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.032 0.016 198.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 92.086 0.261 0.938 0.013 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (1763 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.029 0.015 198.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 101.057 0.237 0.855 0.014 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.018 0.009 197.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 161.882 0.148 0.534 0.022 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 51 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.743 0.872 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.685 14.241 51.269 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 44 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.146 0.089 164.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 16.533 1.452 5.226 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 17 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.396 0.198 199.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 7.410 3.239 11.660 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 97: The Berendsen barostat does not generate any strictly correct ensemble, 97: and should not be used for new production simulations (in our opinion). 97: We recommend using the C-rescale barostat instead. 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: 97: There was 1 WARNING 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.019 0.010 197.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 152.906 0.157 0.565 0.021 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (2089 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 41 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.669 0.835 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.760 13.637 49.094 0.000 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.078 0.039 199.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 37.581 0.639 2.299 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 16 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.376 0.204 184.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 7.205 3.331 11.991 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.680 0.341 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 4.312 5.566 20.039 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.079 0.039 199.3 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 37.278 0.644 2.318 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.052 0.039 132.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 37.624 0.638 2.296 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (2801 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.651 0.326 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 4.504 5.328 19.182 0.001 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.263 0.138 190.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 10.642 2.255 8.118 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.236 0.118 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 12.415 1.933 6.959 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.191 0.096 199.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 15.376 1.561 5.619 0.002 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.085 0.043 199.4 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.386 0.698 2.513 0.005 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.033 0.016 198.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 89.103 0.269 0.970 0.012 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1744 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.118 0.059 199.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 24.784 0.968 3.486 0.003 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 54 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 1.948 0.974 200.0 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 1.507 15.921 57.316 0.000 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.030 0.015 198.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 97.833 0.245 0.883 0.014 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.046 0.023 198.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 63.318 0.379 1.365 0.009 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.103 0.052 199.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 28.391 0.845 3.043 0.004 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: MTTK coupling is deprecated and will soon be removed 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: for current Trotter decomposition methods with vv, nsttcouple and 97: nstpcouple must be equal. Both have been reset to 97: min(nsttcouple,nstpcouple) = 2 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.512 0.256 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 5.731 4.188 15.077 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (2910 ms) 97: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.022 198.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 68.085 0.353 1.269 0.009 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 25 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.604 0.302 199.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 4.860 4.938 17.776 0.001 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.020 0.010 197.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 146.996 0.163 0.588 0.020 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.022 0.011 197.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 131.025 0.183 0.659 0.018 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: NOTE: 32 % of the run time was spent communicating energies, 97: you might want to increase some nst* mdp options 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.063 0.032 198.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 46.030 0.521 1.877 0.006 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Number of degrees of freedom in T-Coupling group System is 33.00 97: 97: There was 1 NOTE 97: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.3-Debian_1 (double precision) 97: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 97: 97: Using 2 MPI threads 97: Using 1 OpenMP thread per tMPI thread 97: 97: 97: NOTE: The number of threads is not equal to the number of (logical) cpus 97: and the -pin option is set to auto: will not pin threads to cpus. 97: This can lead to significant performance degradation. 97: Consider using -pin on (and -pinoffset in case you run multiple jobs). 97: starting mdrun 'Argon' 97: 16 steps, 0.0 ps. 97: Generated 1 of the 1 non-bonded parameter combinations 97: 97: Excluding 1 bonded neighbours molecule type 'Argon' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.119 0.060 199.5 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 24.679 0.972 3.501 0.003 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 97: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (1717 ms) 97: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (42269 ms total) 97: 97: [----------] Global test environment tear-down 97: [==========] 25 tests from 1 test suite ran. (42288 ms total) 97: [ PASSED ] 25 tests. 97/104 Test #97: MdrunCoordinationCouplingTests2Ranks ...... Passed 42.31 sec test 98 Start 98: MdrunCoordinationConstraintsTests1Rank 98: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 98: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 98: Test timeout computed to be: 1920 98: [==========] Running 13 tests from 1 test suite. 98: [----------] Global test environment set-up. 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.029 0.029 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 51.102 0.470 1.691 0.009 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.054 0.054 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 27.119 0.885 3.186 0.005 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.019 0.019 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 78.334 0.306 1.103 0.014 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.023 0.023 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 63.686 0.377 1.357 0.011 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.027 0.027 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 54.688 0.439 1.580 0.009 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.018 0.018 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 81.934 0.293 1.055 0.014 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3075 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.018 0.018 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 80.120 0.300 1.078 0.014 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.064 0.064 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 22.941 1.046 3.766 0.004 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.020 0.020 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 74.076 0.324 1.166 0.013 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.016 0.016 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 93.375 0.257 0.925 0.016 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.095 0.096 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 15.371 1.561 5.621 0.003 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.053 0.053 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 27.556 0.871 3.135 0.005 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3187 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.022 0.022 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 66.475 0.361 1.300 0.012 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.067 0.068 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 21.744 1.104 3.973 0.004 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 133.050 0.180 0.649 0.023 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 98.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 229.539 0.105 0.376 0.040 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 120.848 0.199 0.715 0.021 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 147.665 0.163 0.585 0.026 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3200 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 151.960 0.158 0.569 0.026 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 186.713 0.129 0.463 0.032 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.004 0.004 99.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 328.093 0.073 0.263 0.057 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 227.161 0.106 0.380 0.039 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 170.677 0.141 0.506 0.030 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 203.912 0.118 0.424 0.035 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2867 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 153.054 0.157 0.565 0.027 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 132.631 0.181 0.651 0.023 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.018 0.018 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 81.214 0.296 1.064 0.014 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 112.475 0.213 0.768 0.020 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.034 0.034 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 43.045 0.558 2.007 0.007 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 113.432 0.212 0.762 0.020 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3026 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 207.392 0.116 0.417 0.036 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.005 0.005 99.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 278.672 0.086 0.310 0.048 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 174.289 0.138 0.496 0.030 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.041 0.041 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 35.861 0.669 2.409 0.006 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.018 0.018 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 83.326 0.288 1.037 0.014 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.063 0.063 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 23.457 1.023 3.683 0.004 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3036 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.029 0.030 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 49.785 0.482 1.735 0.009 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.017 0.017 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 88.668 0.271 0.974 0.015 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 103.279 0.232 0.837 0.018 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 154.401 0.155 0.560 0.027 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.020 0.020 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 73.887 0.325 1.169 0.013 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.005 0.005 99.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 306.010 0.078 0.282 0.053 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3000 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 258.154 0.093 0.335 0.045 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 143.573 0.167 0.602 0.025 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.054 0.054 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 27.035 0.888 3.196 0.005 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 108.191 0.222 0.799 0.019 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.075 0.075 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 19.522 1.229 4.426 0.003 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 176.471 0.136 0.490 0.031 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3507 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 137.827 0.174 0.627 0.024 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 147.938 0.162 0.584 0.026 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 153.727 0.156 0.562 0.027 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 157.770 0.152 0.548 0.027 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.012 0.012 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 123.476 0.194 0.700 0.021 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.015 0.015 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 96.109 0.250 0.899 0.017 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2554 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.006 0.006 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 254.108 0.094 0.340 0.044 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.005 0.005 99.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 322.308 0.074 0.268 0.056 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 140.933 0.170 0.613 0.024 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.118 0.118 100.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 12.453 1.927 6.938 0.002 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 108.364 0.221 0.797 0.019 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.035 0.035 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 41.844 0.574 2.065 0.007 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (3071 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.021 0.021 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 68.914 0.348 1.254 0.012 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.009 0.009 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 168.783 0.142 0.512 0.029 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 177.749 0.135 0.486 0.031 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.022 0.022 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 67.345 0.356 1.283 0.012 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.031 0.032 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 46.627 0.515 1.853 0.008 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 146.789 0.163 0.589 0.025 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (3112 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.014 0.014 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 106.544 0.225 0.811 0.018 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.018 0.018 99.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 81.945 0.293 1.054 0.014 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.007 0.007 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 214.820 0.112 0.402 0.037 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 110.724 0.217 0.780 0.019 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.010 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 145.438 0.165 0.594 0.025 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.015 0.016 98.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 94.710 0.253 0.912 0.016 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2810 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 135.113 0.178 0.639 0.023 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.008 0.008 99.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 173.881 0.138 0.497 0.030 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.010 0.011 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 139.832 0.172 0.618 0.024 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.013 0.013 99.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 116.935 0.205 0.739 0.020 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.081 0.081 99.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 18.035 1.331 4.791 0.003 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 98: 98: Using 1 MPI thread 98: Using 1 OpenMP thread 98: 98: 98: NOTE: Thread affinity was not set. 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.011 0.011 99.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 138.319 0.174 0.625 0.024 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2774 ms) 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (39226 ms total) 98: 98: [----------] Global test environment tear-down 98: [==========] 13 tests from 1 test suite ran. (39246 ms total) 98: [ PASSED ] 13 tests. 98/104 Test #98: MdrunCoordinationConstraintsTests1Rank .... Passed 39.29 sec test 99 Start 99: MdrunCoordinationConstraintsTests2Ranks 99: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 99: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 99: Test timeout computed to be: 1920 99: [==========] Running 13 tests from 1 test suite. 99: [----------] Global test environment set-up. 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.6%. 99: The balanceable part of the MD step is 50%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: NOTE: 48 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.033 0.016 199.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 89.479 0.268 0.966 0.016 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.8%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 48 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.030 0.015 199.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 98.017 0.245 0.881 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.0%. 99: The balanceable part of the MD step is 36%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: NOTE: 49 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.038 0.019 199.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 77.720 0.309 1.112 0.013 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.0%. 99: The balanceable part of the MD step is 35%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: NOTE: 48 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.024 0.012 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 123.428 0.194 0.700 0.021 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.0%. 99: The balanceable part of the MD step is 33%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 19 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 14 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.072 0.552 194.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 2.661 9.019 32.468 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.0%. 99: The balanceable part of the MD step is 33%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 18 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 14 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.088 0.546 199.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 2.690 8.922 32.118 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (5638 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.3%. 99: The balanceable part of the MD step is 53%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.2%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.017 0.009 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 167.112 0.144 0.517 0.029 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.7%. 99: The balanceable part of the MD step is 2%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 42 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 28 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.048 0.024 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 60.415 0.397 1.430 0.010 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.5%. 99: The balanceable part of the MD step is 36%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.9%. 99: 99: 99: NOTE: 44 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.011 0.006 195.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 265.154 0.091 0.326 0.046 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.7%. 99: The balanceable part of the MD step is 34%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.2%. 99: 99: 99: NOTE: 68 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.044 0.038 115.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 38.845 0.618 2.224 0.007 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.9%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.006 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 229.856 0.104 0.376 0.040 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 3.4%. 99: The balanceable part of the MD step is 35%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.2%. 99: 99: 99: NOTE: 48 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.033 0.016 199.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 89.636 0.268 0.964 0.016 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4002 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.7%. 99: The balanceable part of the MD step is 53%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 159.230 0.151 0.543 0.028 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.6%. 99: 99: 99: NOTE: 54 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.013 0.007 197.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 221.246 0.108 0.391 0.038 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.1%. 99: The balanceable part of the MD step is 41%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: NOTE: 47 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 188.741 0.127 0.458 0.033 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.8%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: NOTE: 53 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.037 0.019 199.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 78.602 0.305 1.099 0.014 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.0%. 99: The balanceable part of the MD step is 48%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.0%. 99: 99: 99: NOTE: 14 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: NOTE: 37 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.456 0.744 195.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.975 12.155 43.756 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.4%. 99: The balanceable part of the MD step is 39%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.9%. 99: 99: 99: NOTE: 72 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.038 0.035 108.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 41.922 0.572 2.061 0.007 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3914 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 30 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.711 0.856 200.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.716 13.982 50.335 0.000 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 67 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.102 0.051 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 28.771 0.834 3.003 0.005 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.045 0.023 199.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 64.436 0.372 1.341 0.011 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 198.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 157.800 0.152 0.548 0.027 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.024 0.012 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 122.952 0.195 0.703 0.021 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.031 0.016 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 93.472 0.257 0.924 0.016 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (4975 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.021 0.011 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 138.408 0.173 0.624 0.024 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 41 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.029 0.015 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 98.872 0.243 0.874 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 35 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.552 0.792 196.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.855 12.939 46.579 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.007 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 199.285 0.120 0.434 0.035 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 203.411 0.118 0.425 0.035 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.008 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 179.924 0.133 0.480 0.031 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3934 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 43 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.052 0.026 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 56.438 0.425 1.531 0.010 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.024 0.012 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 121.928 0.197 0.709 0.021 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.023 0.012 194.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 122.419 0.196 0.706 0.021 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.014 0.007 198.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 214.771 0.112 0.402 0.037 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 56 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.085 0.066 128.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 22.135 1.084 3.903 0.004 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.029 0.015 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 101.254 0.237 0.853 0.018 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2808 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 22 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.061 0.031 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 47.955 0.500 1.802 0.008 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.032 0.016 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 90.362 0.266 0.956 0.016 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.025 0.012 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 119.004 0.202 0.726 0.021 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.030 0.015 199.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 96.513 0.249 0.895 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 41 % of the run time was spent in domain decomposition, 99: 0 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.076 0.038 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 38.472 0.624 2.246 0.007 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.007 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 199.130 0.121 0.434 0.035 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4028 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 111.102 0.216 0.778 0.019 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 151.292 0.159 0.571 0.026 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.146 0.073 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 20.126 1.193 4.293 0.003 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.030 0.015 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 96.547 0.249 0.895 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.016 0.020 79.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 71.778 0.334 1.204 0.012 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.025 0.012 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 118.189 0.203 0.731 0.021 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3680 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.025 0.012 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 118.515 0.203 0.729 0.021 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 27 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.960 0.996 196.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 1.475 16.273 58.581 0.000 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.022 0.011 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 132.493 0.181 0.652 0.023 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 114.114 0.210 0.757 0.020 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.015 0.008 195.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 187.551 0.128 0.461 0.033 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.056 0.028 199.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 51.906 0.462 1.665 0.009 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (4597 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.6%. 99: The balanceable part of the MD step is 57%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.4%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.034 0.017 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 86.877 0.276 0.995 0.015 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.8%. 99: The balanceable part of the MD step is 58%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 112.010 0.214 0.771 0.019 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 4. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 4. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.0%. 99: The balanceable part of the MD step is 47%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.0%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 197.5 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 161.787 0.148 0.534 0.028 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.1%. 99: The balanceable part of the MD step is 45%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.0%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.047 0.023 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 62.553 0.384 1.381 0.011 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.5%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: NOTE: 14 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.059 0.029 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 49.883 0.481 1.732 0.009 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 100. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 100. 99: 99: 99: There were 4 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 2.7%. 99: The balanceable part of the MD step is 46%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 1.2%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.046 0.023 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 63.072 0.381 1.370 0.011 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (3094 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.5%. 99: The balanceable part of the MD step is 60%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.3%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.039 0.020 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 74.149 0.324 1.165 0.013 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.4%. 99: The balanceable part of the MD step is 57%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.8%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.025 0.013 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 114.416 0.210 0.755 0.020 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.0%. 99: The balanceable part of the MD step is 53%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.030 0.015 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 98.329 0.244 0.879 0.017 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.7%. 99: The balanceable part of the MD step is 50%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.9%. 99: 99: 99: NOTE: 46 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.153 0.079 192.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 18.515 1.296 4.666 0.003 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 0.9%. 99: The balanceable part of the MD step is 51%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.5%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.033 0.017 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 88.917 0.270 0.972 0.015 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: NVE simulation: will use the initial temperature of 398.997 K for 99: determining the Verlet buffer size 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Can not increase nstlist because an NVE ensemble is used 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: 99: Dynamic load balancing report: 99: DLB was off during the run due to low measured imbalance. 99: Average load imbalance: 1.3%. 99: The balanceable part of the MD step is 51%, load imbalance is computed from this. 99: Part of the total run time spent waiting due to load imbalance: 0.7%. 99: 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.051 0.026 199.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 57.331 0.419 1.507 0.010 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (3562 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.051 0.026 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 57.307 0.419 1.508 0.010 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.018 0.009 197.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 159.646 0.150 0.541 0.028 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.019 0.010 196.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 149.134 0.161 0.579 0.026 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.042 0.023 186.1 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 64.401 0.373 1.342 0.011 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.043 0.022 198.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 67.097 0.358 1.288 0.012 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 99: COM removal frequency is set to (5). 99: Other settings require a global communication frequency of 2. 99: Note that this will require additional global communication steps, 99: which will reduce performance when using multiple ranks. 99: Consider setting nstcomm to a multiple of 2. 99: 99: 99: There were 3 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.048 0.024 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 60.314 0.398 1.433 0.010 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3078 ms) 99: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.035 0.018 198.4 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 83.750 0.287 1.032 0.015 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (1) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.041 0.021 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 70.789 0.339 1.221 0.012 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: Setting nstcalcenergy (100) equal to nstenergy (4) 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 24 % of the run time was spent communicating energies, 99: you might want to increase some nst* mdp options 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.121 0.061 198.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 24.139 0.994 3.579 0.004 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.027 0.014 197.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 107.684 0.223 0.802 0.019 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.060 0.030 199.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 48.772 0.492 1.772 0.008 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 99: setting nstcomm equal to nstcalcenergy for less overhead 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 27.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There were 2 NOTEs 99: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 99: 99: Using 2 MPI threads 99: Using 1 OpenMP thread per tMPI thread 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'spc2' 99: 16 steps, 0.0 ps. 99: Generated 330891 of the 330891 non-bonded parameter combinations 99: 99: Generated 330891 of the 330891 1-4 parameter combinations 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.033 0.017 198.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 88.036 0.273 0.981 0.015 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 99: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 99: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2591 ms) 99: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (49908 ms total) 99: 99: [----------] Global test environment tear-down 99: [==========] 13 tests from 1 test suite ran. (49923 ms total) 99: [ PASSED ] 13 tests. 99/104 Test #99: MdrunCoordinationConstraintsTests2Ranks ... Passed 49.96 sec test 100 Start 100: MdrunFEPTests 100: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 100: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 100: Test timeout computed to be: 600 100: [==========] Running 14 tests from 2 test suites. 100: [----------] Global test environment set-up. 100: [----------] 2 tests from ExpandedEnsembleTest 100: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 16 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.024 0.012 199.3 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 121.413 0.198 0.712 0.051 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 100: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 100: 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 100: 100: Writing final coordinates. 100: 100: NOTE: 12 % of the run time was spent in pair search, 100: you might want to increase nstlist (this has no effect on accuracy) 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.196 0.098 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 7.931 3.026 10.893 0.003 100: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (166 ms) 100: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 79.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 100: You are using a plain Coulomb cut-off, which might produce artifacts. 100: You might want to consider using PME electrostatics. 100: 100: 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun '30 atom system in water' 100: 1 steps, 0.0 ps. 100: Generated 2485 of the 2485 non-bonded parameter combinations 100: 100: Generated 2485 of the 2485 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'nonanol' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/nonanol_vacuo.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.080 0.040 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 4.330 5.542 19.952 0.002 100: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (77 ms) 100: [----------] 2 tests from ExpandedEnsembleTest (243 ms total) 100: 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 1610575787 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.93 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.178 0.089 199.9 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 20.330 1.181 4.250 0.042 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 100: 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (215 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 803470333 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.93 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.181 0.090 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 20.052 1.197 4.309 0.041 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (249 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 515375063 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.93 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.722 0.361 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 5.024 4.777 17.196 0.010 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (471 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 155]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 155]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to -543293569 100: 100: Generated 171 of the 171 non-bonded parameter combinations 100: 100: Generated 171 of the 171 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 358.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 1 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.95 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: NOTE: 14 % of the run time was spent in domain decomposition, 100: 9 % of the run time was spent in pair search, 100: you might want to increase nstlist (this has no effect on accuracy) 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.216 0.108 199.9 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 16.813 1.427 5.139 0.035 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (183 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: NOTE 3 [file topol.top, line 165]: 100: System has non-zero total charge: 1.000000 100: Total charge should normally be an integer. See 100: https://manual.gromacs.org/current/user-guide/floating-point.html 100: for discussion on how close it should be to an integer. 100: 100: 100: 100: 100: WARNING 2 [file topol.top, line 165]: 100: You are using Ewald electrostatics in a system with net charge. This can 100: lead to severe artifacts, such as ions moving into regions with low 100: dielectric, due to the uniform background charge. We suggest to 100: neutralize your system with counter ions, possibly in combination with a 100: physiological salt concentration. 100: 100: Setting the LD random seed to -13767841 100: 100: Generated 190 of the 190 non-bonded parameter combinations 100: 100: Generated 190 of the 190 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'NA' 100: 100: turning H bonds into constraints... 100: 100: Excluding 1 bonded neighbours molecule type 'CL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'CL' 100: 100: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 100: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 100: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 100: Charge 100: J. Chem. Theory Comput. (2014) 100: https://doi.org/10.1021/ct400626b 100: -------- -------- --- Thank You --- -------- -------- 100: 100: Number of degrees of freedom in T-Coupling group System is 361.00 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 5 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 5 NOTEs 100: 100: There were 2 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: There are: 2 Ion residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 100: 100: Estimate for the relative computational load of the PME mesh part: 0.95 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.150 0.075 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 24.144 0.994 3.579 0.050 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (114 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 100: For proper sampling of the (nearly) decoupled state, stochastic dynamics 100: should be used 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 100: and vdw_modifier=Force-switch 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 4 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 100 steps, 0.1 ps. 100: Setting the LD random seed to -134401027 100: 100: Generated 153 of the 153 non-bonded parameter combinations 100: 100: Generated 153 of the 153 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Coupling 1 copies of molecule type 'ASN' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.93 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.529 0.765 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 11.413 2.103 7.570 0.023 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (924 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There were 11 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -34097153 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.93 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.335 0.667 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 2.719 8.828 31.779 0.006 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (852 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: 100: WARNING 2 [file topol.top, line 72]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 8 1'. 100: 100: 100: WARNING 3 [file topol.top, line 73]: 100: No default Bond types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '7 9 1'. 100: 100: 100: WARNING 4 [file topol.top, line 98]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '6 5 7 1'. 100: 100: 100: WARNING 5 [file topol.top, line 99]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 8 1'. 100: 100: 100: WARNING 6 [file topol.top, line 100]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '5 7 9 1'. 100: 100: 100: WARNING 7 [file topol.top, line 101]: 100: No default Angle types for perturbed atoms in interaction, using normal 100: values. The interaction was 100: '8 7 9 1'. 100: 100: 100: WARNING 8 [file topol.top, line 111]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 8 3'. 100: 100: 100: WARNING 9 [file topol.top, line 112]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '1 5 7 9 3'. 100: 100: 100: WARNING 10 [file topol.top, line 113]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 8 3'. 100: 100: 100: WARNING 11 [file topol.top, line 114]: 100: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 100: normal values. The interaction was 100: '6 5 7 9 3'. 100: 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: Removing center of mass motion in the presence of position restraints 100: might cause artifacts. When you are using position restraints to 100: equilibrate a macro-molecule, the artifacts are usually negligible. 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There were 11 WARNINGs 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 690723581 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.93 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 1.165 0.583 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 3.114 7.707 27.746 0.006 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (775 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 2 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 1459583935 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.87 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.510 0.255 199.9 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 7.114 3.374 12.145 0.015 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (380 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: There was 1 NOTE 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.697 0.348 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 5.206 4.610 16.595 0.011 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: Setting the LD random seed to -1342294201 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.87 100: 100: This run will generate roughly 0 Mb of data 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (529 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to -8913409 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.93 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.881 0.441 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 4.119 5.827 20.977 0.008 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (552 ms) 100: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: With PME there is a minor soft core effect present at the cut-off, 100: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 100: energy conservation, but usually other effects dominate. With a common 100: sigma value of 0.34 nm the fraction of the particle-particle potential at 100: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 100: 100: 100: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The Berendsen thermostat does not generate the correct kinetic energy 100: distribution, and should not be used for new production simulations (in 100: our opinion). We would recommend the V-rescale thermostat. 100: 100: Generating 1-4 interactions: fudge = 0.5 100: Number of degrees of freedom in T-Coupling group System is 355.00 100: 100: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: The optimal PME mesh load for parallel simulations is below 0.5 100: and for highly parallel simulations between 0.25 and 0.33, 100: for higher performance, increase the cut-off and the PME grid spacing. 100: 100: 100: 100: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 100: For free energy simulations, the optimal load limit increases from 0.5 to 100: 0.667 100: 100: 100: 100: There were 3 NOTEs 100: 100: There was 1 WARNING 100: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 100: Changing nstlist from 10 to 100, rlist from 1 to 1 100: 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'AA' 100: 20 steps, 0.0 ps. 100: Setting the LD random seed to 1589591966 100: 100: Generated 136 of the 136 non-bonded parameter combinations 100: 100: Generated 136 of the 136 1-4 parameter combinations 100: 100: Excluding 3 bonded neighbours molecule type 'ASN' 100: 100: turning H bonds into constraints... 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: turning H bonds into constraints... 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 100: Analysing residue names: 100: There are: 1 Protein residues 100: There are: 56 Water residues 100: Analysing Protein... 100: 100: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 100: 100: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 100: 100: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: Calculating fourier grid dimensions for X Y Z 100: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 100: 100: Estimate for the relative computational load of the PME mesh part: 0.88 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.613 0.307 200.0 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 5.918 4.056 14.600 0.012 100: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 100: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (414 ms) 100: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (5675 ms total) 100: 100: [----------] Global test environment tear-down 100: [==========] 14 tests from 2 test suites ran. (5949 ms total) 100: [ PASSED ] 14 tests. 100/104 Test #100: MdrunFEPTests ............................. Passed 5.99 sec test 101 Start 101: MdrunPullTests 101: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 101: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 101: Test timeout computed to be: 600 101: [==========] Running 4 tests from 1 test suite. 101: [----------] Global test environment set-up. 101: [----------] 4 tests from PullTest/PullIntegrationTest 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.600 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2026.3-Debian_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.213 0.107 199.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 17.033 1.409 5.073 0.128 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (394 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.301 nm 0.400 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2026.3-Debian_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.140 0.070 199.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 25.861 0.928 3.341 0.194 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (641 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Pull group 3 'r_3' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1292.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.357 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.500 nm 101: 1 3 2 101: 3 3 8 0.331 nm 0.400 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2026.3-Debian_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.220 0.110 199.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 16.510 1.454 5.233 0.124 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (464 ms) 101: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 101: Generating 1-4 interactions: fudge = 0.5 101: Pull group 1 'r_1' has 3 atoms 101: Pull group 2 'r_2' has 3 atoms 101: Number of degrees of freedom in T-Coupling group System is 1293.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 101: NVE simulation: will use the initial temperature of 303.122 K for 101: determining the Verlet buffer size 101: 101: Pull group natoms pbc atom distance at start reference at t=0 101: 1 3 2 101: 2 3 5 0.575 nm 0.000 nm 101: 0.050 nm 0.000 nm 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2026.3-Debian_1 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'spc2' 101: 20 steps, 0.0 ps. 101: Generated 330891 of the 330891 non-bonded parameter combinations 101: 101: Generated 330891 of the 330891 1-4 parameter combinations 101: 101: Excluding 2 bonded neighbours molecule type 'SOL' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc216.gro' 101: 101: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 101: 101: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 101: 101: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 101: 101: Note that mdrun will redetermine rlist based on the actual pair-list setup 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.214 0.107 199.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 16.938 1.417 5.101 0.127 101: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 101: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (415 ms) 101: [----------] 4 tests from PullTest/PullIntegrationTest (1916 ms total) 101: 101: [----------] Global test environment tear-down 101: [==========] 4 tests from 1 test suite ran. (1923 ms total) 101: [ PASSED ] 4 tests. 101/104 Test #101: MdrunPullTests ............................ Passed 1.94 sec test 102 Start 102: MdrunRotationTests 102: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 102: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 102: Test timeout computed to be: 600 102: [==========] Running 12 tests from 1 test suite. 102: [----------] Global test environment set-up. 102: [----------] 12 tests from RotationWorks/RotationTest 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 102: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: trr version: GMX_trn_file (single precision) 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 1300233903 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 365.084 0.066 0.473 0.008 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (30 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 102: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1317033601 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.012 0.006 198.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 770.880 0.031 0.224 0.018 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (21 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 102: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1275627661 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: NOTE: 18 % of the run time was spent in pair search, 102: you might want to increase nstlist (this has no effect on accuracy) 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.195 0.098 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 46.071 0.521 3.751 0.001 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (109 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 102: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1544241668 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.016 0.008 198.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 557.322 0.043 0.310 0.013 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (19 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 102: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -322052161 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: NOTE: 15 % of the run time was spent in pair search, 102: you might want to increase nstlist (this has no effect on accuracy) 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.222 0.111 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 40.422 0.594 4.275 0.001 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (131 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 102: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 535287735 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: NOTE: 16 % of the run time was spent in pair search, 102: you might want to increase nstlist (this has no effect on accuracy) 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.221 0.110 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 40.689 0.590 4.247 0.001 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (129 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 102: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -539017217 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.019 0.009 198.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 473.710 0.051 0.365 0.011 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (19 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 102: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 2143156185 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.018 0.009 198.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 488.583 0.049 0.354 0.011 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (19 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 102: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to 2012528631 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.034 0.017 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 259.533 0.092 0.666 0.006 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (27 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 102: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -554172481 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: NOTE: 19 % of the run time was spent in pair search, 102: you might want to increase nstlist (this has no effect on accuracy) 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.240 0.120 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 37.495 0.640 4.609 0.001 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (139 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 102: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1628145747 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: NOTE: 16 % of the run time was spent in pair search, 102: you might want to increase nstlist (this has no effect on accuracy) 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.193 0.097 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 46.545 0.516 3.712 0.001 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (120 ms) 102: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 102: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 102: Rotation group 0 'system' has 4 atoms 102: Number of degrees of freedom in T-Coupling group rest is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 102: NVE simulation with an initial temperature of zero: will use a Verlet 102: buffer of 10%. Check your energy drift! 102: 102: Enforced rotation: group 0 has 4 reference positions. 102: Reading them from /build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/rotref.0.trr. 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2026.3-Debian_1 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 102: 25 steps, 0.1 ps. 102: Setting the LD random seed to -1090715665 102: 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonA' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonB' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonC' 102: 102: Excluding 1 bonded neighbours molecule type 'ArgonD' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.024 0.012 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 372.172 0.064 0.464 0.009 102: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 102: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 102: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (22 ms) 102: [----------] 12 tests from RotationWorks/RotationTest (792 ms total) 102: 102: [----------] Global test environment tear-down 102: [==========] 12 tests from 1 test suite ran. (812 ms total) 102: [ PASSED ] 12 tests. 102/104 Test #102: MdrunRotationTests ........................ Passed 0.84 sec test 103 Start 103: MdrunSimulatorComparison 103: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 103: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 103: Test timeout computed to be: 600 103: [==========] Running 94 tests from 4 test suites. 103: [----------] Global test environment set-up. 103: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 11 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.161 0.081 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 18.185 1.320 4.751 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: NOTE: 10 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.165 0.082 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 17.838 1.345 4.844 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 103: 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (178 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.068 0.034 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 43.166 0.556 2.002 0.006 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: NOTE: 14 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.265 0.132 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 11.100 2.162 7.784 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (185 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.147 0.074 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 19.947 1.203 4.331 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.170 0.085 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 17.264 1.390 5.005 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (176 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 132.623 0.181 0.651 0.018 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.014 0.007 198.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 208.841 0.115 0.414 0.029 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (31 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 159.407 0.151 0.542 0.022 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.011 198.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 138.743 0.173 0.623 0.019 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (31 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.101 0.051 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 28.992 0.828 2.980 0.004 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.182 0.091 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 16.088 1.492 5.371 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (166 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There were 2 WARNINGs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.179 0.089 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 16.435 1.460 5.257 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.021 0.011 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 136.617 0.176 0.632 0.019 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (115 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.028 0.014 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 103.056 0.233 0.838 0.014 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: NOTE: 13 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.045 0.022 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 65.380 0.367 1.321 0.009 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (56 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: MTTK coupling is deprecated and will soon be removed 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.027 0.014 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 106.756 0.225 0.809 0.015 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 197.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 185.404 0.129 0.466 0.026 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (33 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.256 0.128 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 11.449 2.096 7.547 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.164 0.082 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 17.896 1.341 4.828 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (230 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.034 0.017 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 85.447 0.281 1.011 0.012 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.157 0.079 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 18.663 1.286 4.630 0.003 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (108 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 103: MTTK coupling is deprecated and will soon be removed 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.025 0.013 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 116.559 0.206 0.741 0.016 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.027 0.014 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 108.478 0.221 0.796 0.015 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (37 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.184 0.092 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 15.990 1.501 5.403 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: NOTE: 34 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.046 0.023 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 63.279 0.379 1.365 0.009 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (137 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.014 0.007 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 209.651 0.114 0.412 0.029 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.025 0.013 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 116.988 0.205 0.739 0.016 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (31 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.293 0.147 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 10.009 2.398 8.632 0.001 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.157 0.078 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 18.756 1.280 4.607 0.003 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (248 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: Center of mass removal not necessary for Andersen. All velocities of 103: coupled groups are rerandomized periodically, so flying ice cube errors 103: will not occur. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.188 0.094 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 15.590 1.539 5.542 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.270 0.135 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 10.861 2.210 7.955 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (253 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: Center of mass removal not necessary for Andersen. All velocities of 103: coupled groups are rerandomized periodically, so flying ice cube errors 103: will not occur. 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.016 0.008 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 179.651 0.134 0.481 0.025 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.221 0.111 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 13.283 1.807 6.505 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (144 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: Center of mass removal not necessary for Andersen. All velocities of 103: coupled groups are rerandomized periodically, so flying ice cube errors 103: will not occur. 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.297 0.149 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 9.888 2.427 8.738 0.001 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.301 0.151 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 9.741 2.464 8.870 0.001 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (334 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 23 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.068 0.034 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 43.314 0.554 1.995 0.008 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.308 0.154 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 9.519 2.521 9.077 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (791 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.216 0.108 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 13.615 1.763 6.346 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.361 0.181 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 8.123 2.955 10.636 0.001 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (727 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.228 0.114 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 12.878 1.864 6.709 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.099 0.050 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 29.553 0.812 2.924 0.005 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (781 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.252 0.126 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 11.638 2.062 7.424 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.214 0.107 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 13.689 1.753 6.312 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (824 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.200 0.100 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 14.644 1.639 5.900 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.328 0.164 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 8.942 2.684 9.662 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (569 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.009 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 155.775 0.154 0.555 0.027 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.037 0.018 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 80.093 0.300 1.079 0.014 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (614 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There were 2 WARNINGs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.009 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 157.689 0.152 0.548 0.027 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.020 0.010 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 146.024 0.164 0.592 0.025 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (325 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.054 0.027 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 54.719 0.439 1.579 0.009 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.014 0.007 198.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 209.622 0.114 0.412 0.036 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (598 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.310 0.155 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 9.474 2.533 9.120 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.040 0.020 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 72.632 0.330 1.190 0.013 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (557 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.086 0.043 199.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 33.967 0.707 2.544 0.006 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 198.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 158.313 0.152 0.546 0.027 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (658 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.019 0.010 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 152.618 0.157 0.566 0.026 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.114 0.057 199.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 25.730 0.933 3.358 0.004 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (431 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.237 0.119 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 12.387 1.937 6.975 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.049 0.024 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 60.103 0.399 1.438 0.010 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (751 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 103: Andersen temperature control methods assume nsttcouple = 1; there is no 103: need for larger nsttcouple > 1, since no global parameters are computed. 103: nsttcouple has been reset to 1 103: 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.070 0.035 199.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 41.877 0.573 2.063 0.007 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.042 0.021 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 69.105 0.347 1.250 0.012 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (655 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 103: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 103: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (10791 ms total) 103: 103: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.010 0.005 198.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 287.127 0.084 0.301 0.040 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.024 0.012 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 124.105 0.193 0.696 0.017 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (29 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.011 0.005 198.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 277.167 0.087 0.312 0.038 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.012 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 127.686 0.188 0.677 0.018 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (34 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 103: NVE simulation: will use the initial temperature of 68.810 K for 103: determining the Verlet buffer size 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 11 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.254 0.127 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 11.563 2.076 7.472 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: NOTE: 10 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.231 0.115 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 12.722 1.886 6.791 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (275 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.135 0.067 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 21.795 1.101 3.964 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.023 0.012 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 124.802 0.192 0.692 0.017 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (97 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 113.704 0.211 0.760 0.016 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.039 0.020 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 75.108 0.320 1.150 0.010 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (47 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.133 0.067 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 22.019 1.090 3.924 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 162.574 0.148 0.531 0.023 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (107 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.261 0.130 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 11.258 2.132 7.674 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.047 0.023 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 62.807 0.382 1.376 0.009 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (177 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.257 0.129 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 11.415 2.102 7.569 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.219 0.109 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 13.420 1.788 6.438 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (262 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 19 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.030 0.015 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 98.258 0.244 0.879 0.014 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.025 0.012 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 118.619 0.202 0.728 0.016 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (55 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There were 2 WARNINGs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.206 0.103 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 14.249 1.684 6.063 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.213 0.106 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 13.816 1.737 6.254 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (232 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There was 1 NOTE 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.129 0.065 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 22.752 1.055 3.797 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.017 0.009 198.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 166.958 0.144 0.517 0.023 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (90 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.035 0.017 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 84.674 0.283 1.020 0.012 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.254 0.127 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 11.545 2.079 7.484 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (162 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.010 0.005 198.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 290.156 0.083 0.298 0.040 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.010 0.005 197.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 299.087 0.080 0.289 0.042 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (34 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.022 0.011 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 133.372 0.180 0.648 0.019 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 198.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 165.670 0.145 0.522 0.023 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (32 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 33.00 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: Generated 1 of the 1 non-bonded parameter combinations 103: 103: Excluding 1 bonded neighbours molecule type 'Argon' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/argon12.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.178 0.089 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 16.532 1.452 5.226 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Argon' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.132 0.066 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 22.214 1.080 3.889 0.003 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (179 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.041 0.021 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 71.010 0.338 1.217 0.012 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.013 0.007 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 222.742 0.108 0.388 0.039 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (339 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.076 0.038 199.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 38.676 0.621 2.234 0.007 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.010 0.005 198.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 292.832 0.082 0.295 0.051 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (461 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: NVE simulation: will use the initial temperature of 398.997 K for 103: determining the Verlet buffer size 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 11 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.220 0.110 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 13.339 1.799 6.477 0.002 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.018 0.009 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 158.240 0.152 0.546 0.027 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (706 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 12 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.147 0.073 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 19.991 1.201 4.322 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.051 0.026 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 57.513 0.417 1.502 0.010 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (408 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.052 0.026 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 55.927 0.429 1.545 0.010 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.011 0.005 197.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 271.523 0.088 0.318 0.047 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (639 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.037 0.019 199.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 79.105 0.303 1.092 0.014 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.038 0.019 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 76.620 0.313 1.128 0.013 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (341 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.160 0.080 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 18.382 1.306 4.700 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.144 0.072 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 20.422 1.175 4.231 0.004 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (494 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.081 0.041 199.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 35.985 0.667 2.401 0.006 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: NOTE: 12 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.139 0.069 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 21.193 1.132 4.077 0.004 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (624 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.099 0.049 199.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 29.689 0.808 2.910 0.005 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.352 0.176 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 8.346 2.875 10.352 0.001 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (755 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: 103: WARNING 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There were 2 WARNINGs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.031 0.015 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 94.854 0.253 0.911 0.016 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.037 0.018 199.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 80.207 0.299 1.077 0.014 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (606 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: The Berendsen thermostat does not generate the correct kinetic energy 103: distribution, and should not be used for new production simulations (in 103: our opinion). We would recommend the V-rescale thermostat. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 2 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.180 0.090 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 16.317 1.471 5.295 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.029 0.014 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 102.397 0.234 0.844 0.018 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (536 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.156 0.078 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 18.864 1.272 4.580 0.003 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.152 0.076 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 19.338 1.241 4.468 0.003 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (553 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.055 0.027 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 53.768 0.446 1.607 0.009 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.041 0.020 199.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 72.121 0.333 1.198 0.013 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (611 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: 103: WARNING 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: The Berendsen barostat does not generate any strictly correct ensemble, 103: and should not be used for new production simulations (in our opinion). 103: We recommend using the C-rescale barostat instead. 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: 103: There was 1 WARNING 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.056 0.028 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 52.375 0.458 1.650 0.009 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.013 0.007 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 216.480 0.111 0.399 0.038 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (636 ms) 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Number of degrees of freedom in T-Coupling group System is 27.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 330891 of the 330891 non-bonded parameter combinations 103: 103: Generated 330891 of the 330891 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/tip3p5.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.139 0.069 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 21.190 1.133 4.077 0.004 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 103: 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.242 0.121 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 12.137 1.977 7.119 0.002 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (506 ms) 103: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (10044 ms total) 103: 103: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Pull group 1 'FirstWaterMolecule' has 3 atoms 103: Pull group 2 'SecondWaterMolecule' has 3 atoms 103: Number of degrees of freedom in T-Coupling group System is 9.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: NVE simulation: will use the initial temperature of 2573.591 K for 103: determining the Verlet buffer size 103: 103: Pull group natoms pbc atom distance at start reference at t=0 103: 1 3 2 103: 2 3 5 1.112 nm 1.000 nm 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 3 of the 3 non-bonded parameter combinations 103: 103: Generated 3 of the 3 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.194 0.097 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 15.121 1.587 5.714 0.001 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.074 0.037 199.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 39.584 0.606 2.183 0.003 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (156 ms) 103: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (157 ms total) 103: 103: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 103: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Generating 1-4 interactions: fudge = 0.5 103: Pull group 1 'FirstWaterMolecule' has 3 atoms 103: Pull group 2 'SecondWaterMolecule' has 3 atoms 103: Number of degrees of freedom in T-Coupling group System is 9.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 103: NVE simulation: will use the initial temperature of 2573.591 K for 103: determining the Verlet buffer size 103: 103: Pull group natoms pbc atom distance at start reference at t=0 103: 1 3 2 103: 2 3 5 1.112 nm 1.000 nm 103: 103: There were 2 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: Generated 3 of the 3 non-bonded parameter combinations 103: 103: Generated 3 of the 3 1-4 parameter combinations 103: 103: Excluding 2 bonded neighbours molecule type 'SOL' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/spc2.gro' 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 11 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.167 0.084 199.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 17.585 1.365 4.913 0.001 103: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.3-Debian_1 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Using 1 MPI thread 103: Using 2 OpenMP threads 103: 103: 103: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 103: modular simulator with an integrator other than VV 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'spc2' 103: 16 steps, 0.0 ps. 103: 103: Writing final coordinates. 103: 103: NOTE: 14 % of the run time was spent in pair search, 103: you might want to increase nstlist (this has no effect on accuracy) 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.182 0.091 199.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 16.131 1.488 5.356 0.001 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 103: Opened /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 103: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 103: 103: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (207 ms) 103: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (207 ms total) 103: 103: [----------] Global test environment tear-down 103: [==========] 94 tests from 4 test suites ran. (21248 ms total) 103: [ PASSED ] 94 tests. 103/104 Test #103: MdrunSimulatorComparison .................. Passed 21.26 sec test 104 Start 104: MdrunVirtualSiteTests 104: Test command: /build/reproducible-path/gromacs-2026.3/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.3/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 104: Working Directory: /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests 104: Test timeout computed to be: 600 104: [==========] Running 37 tests from 2 test suites. 104: [----------] Global test environment set-up. 104: [----------] 1 test from VirtualSiteVelocityTest 104: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 104: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 104: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 104: 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 21.4%. 104: The balanceable part of the MD step is 32%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 6.8%. 104: 104: NOTE: 6.8 % of the available CPU time was lost due to load imbalance 104: in the domain decomposition. 104: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 104: You can also consider manually changing the decomposition (option -dd); 104: e.g. by using fewer domains along the box dimension in which there is 104: considerable inhomogeneity in the simulated system. 104: 104: NOTE: 25 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 10 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 1.020 0.510 200.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.525 15.740 56.666 0.000 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.3-Debian_1 (double precision) 104: trr version: GMX_trn_file (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (1143 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 8.4%. 104: The balanceable part of the MD step is 0%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.0%. 104: 104: 104: NOTE: 60 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 8 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.212 0.106 199.7 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 7.313 3.282 11.814 0.002 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (895 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 3.0%. 104: The balanceable part of the MD step is 36%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 1.1%. 104: 104: 104: NOTE: 56 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.029 0.015 199.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 52.590 0.456 1.643 0.015 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (83 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.020 0.010 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 77.786 0.309 1.111 0.022 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (62 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 67 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.100 0.074 135.2 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 10.539 2.277 8.198 0.003 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (234 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 52 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.035 0.018 199.3 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 44.307 0.542 1.950 0.012 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (46 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 15 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 10 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.864 0.432 200.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.800 13.331 47.990 0.001 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (1048 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 16 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 10 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.848 0.440 192.7 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.767 13.579 48.883 0.000 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (1235 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 104: 1 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 4 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 4 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 24 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 13 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.536 0.284 188.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 2.739 8.762 31.542 0.001 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (1003 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 3.0%. 104: The balanceable part of the MD step is 25%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 0.7%. 104: 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.022 0.011 198.7 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 71.156 0.337 1.214 0.020 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (99 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: NVE simulation with an initial temperature of zero: will use a Verlet 104: buffer of 10%. Check your energy drift! 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Can not increase nstlist because an NVE ensemble is used 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: 104: Dynamic load balancing report: 104: DLB was off during the run due to low measured imbalance. 104: Average load imbalance: 2.4%. 104: The balanceable part of the MD step is 44%, load imbalance is computed from this. 104: Part of the total run time spent waiting due to load imbalance: 1.1%. 104: 104: 104: NOTE: 70 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.041 0.036 112.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 21.409 1.121 4.036 0.006 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (111 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 49 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.031 0.016 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 49.421 0.486 1.748 0.014 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (38 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 11 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 26 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 1.128 0.580 194.5 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.341 17.900 64.442 0.000 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (1160 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.022 0.011 198.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 71.016 0.338 1.217 0.020 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (44 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 49 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.113 0.057 199.8 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 13.734 1.748 6.291 0.004 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (176 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.013 0.007 198.4 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 115.158 0.208 0.750 0.032 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (196 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 46 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.015 0.007 198.5 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 105.586 0.227 0.818 0.029 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (55 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Taking velocities from '/build/reproducible-path/gromacs-2026.3/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 48 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.019 0.010 199.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 81.823 0.293 1.056 0.023 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (47 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 47 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.010 0.005 197.6 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 148.223 0.162 0.583 0.041 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (64 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 34 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 12 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.375 0.188 199.9 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 4.142 5.794 20.860 0.001 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (809 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 104: 104: NOTE 1 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: Setting nstcalcenergy (100) equal to nstenergy (4) 104: 104: Number of degrees of freedom in T-Coupling group System is 45.00 104: 104: NOTE 2 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: There are 6 non-linear virtual site constructions. Their contribution to 104: the energy error is approximated. In most cases this does not affect the 104: error significantly. 104: 104: 104: NOTE 3 [file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 104: You are using a plain Coulomb cut-off, which might produce artifacts. 104: You might want to consider using PME electrostatics. 104: 104: 104: 104: There were 3 NOTEs 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 104: 104: Update groups can not be used for this system because an incompatible virtual site type is used 104: 104: Using 2 MPI threads 104: Using 1 OpenMP thread per tMPI thread 104: 104: 104: NOTE: The number of threads is not equal to the number of (logical) cpus 104: and the -pin option is set to auto: will not pin threads to cpus. 104: This can lead to significant performance degradation. 104: Consider using -pin on (and -pinoffset in case you run multiple jobs). 104: starting mdrun 'Virtual sites test system in vacuo' 104: 8 steps, 0.0 ps. 104: Generated 3 of the 6 non-bonded parameter combinations 104: 104: Excluding 3 bonded neighbours molecule type 'VSTEST' 104: 104: Cleaning up constraints and constant bonded interactions with virtual sites 104: 104: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 104: 104: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 104: 104: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 104: 104: Note that mdrun will redetermine rlist based on the actual pair-list setup 104: 104: This run will generate roughly 0 Mb of data 104: 104: Writing final coordinates. 104: 104: NOTE: 16 % of the run time was spent in domain decomposition, 104: 0 % of the run time was spent in pair search, 104: you might want to increase nstlist (this has no effect on accuracy) 104: 104: NOTE: 8 % of the run time was spent communicating energies, 104: you might want to increase some nst* mdp options 104: 104: Core t (s) Wall t (s) (%) 104: Time: 0.863 0.432 200.0 104: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 104: Performance: 1.801 13.322 47.960 0.001 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.3-Debian_1 (double precision) 104: Reading file /build/reproducible-path/gromacs-2026.3/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.3-Debian_1 (double precision) 104: 104: Reading virtual site types... 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (1089 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 104: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 104: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 104: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (9655 ms total) 104: 104: [----------] Global test environment tear-down 104: [==========] 37 tests from 2 test suites ran. (9663 ms total) 104: [ PASSED ] 37 tests. 104/104 Test #104: MdrunVirtualSiteTests ..................... Passed 9.69 sec 100% tests passed, 0 tests failed out of 104 Label Time Summary: GTest = 600.63 sec*proc (97 tests) IntegrationTest = 313.00 sec*proc (30 tests) MpiTest = 422.86 sec*proc (24 tests) QuickGpuTest = 86.64 sec*proc (25 tests) SlowGpuTest = 465.86 sec*proc (15 tests) SlowTest = 260.66 sec*proc (14 tests) UnitTest = 26.97 sec*proc (53 tests) Total Test time (real) = 351.63 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.3/build/mpi/lib /usr/bin/make -j8 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2026.3/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.3 -B/build/reproducible-path/gromacs-2026.3/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.3/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2026.3/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/selection /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.3/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E 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-DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.3-Debian_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.3 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.3/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.3/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-1 -P /build/reproducible-path/gromacs-2026.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/errhandler.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c 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/build/reproducible-path/gromacs-2026.3/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmm_mdmodule.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvar.cpp [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/binary_information.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 0%] Built target thread_mpi cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmm_mdpoptions.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/dict.c /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/abstractoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmforceproviderbuilder.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o 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/build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvaratoms.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fileio/h5md && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fileio/h5md/h5md.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmoptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 0%] Built target h5md cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/fmm/fmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/widemuldiv.c /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 1%] Built target linearalgebra cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 1%] Built target fmm /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/programs /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/gmx.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 1%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 1%] Built target gmx_objlib /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.3/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/filenameoptionmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 1%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 5%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_meta.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 5%] Built target pulling cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarbias_restraint.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 7%] Built target options /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include 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/build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.3/src/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/taskassignment/resourcedivision.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.3/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.3/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC 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/build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 8%] Built target modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' [ 14%] Built target colvars_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.3/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.3/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.3 /build/reproducible-path/gromacs-2026.3/src/gromacs /build/reproducible-path/gromacs-2026.3/build/mpi /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.3/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.3/build/mpi' cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.3/src/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.3/src -I/build/reproducible-path/gromacs-2026.3/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.3/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.3/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.3/build/mpi/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2026.3/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.3/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd 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